Please note that this guide will be corrected/refined/added to...whenever, is incomplete, and may not feature optimal/best ways to do things until contributors (I hope, though rather unlikely) or I can pull them off with consistency.
Table of Contents
1 - General Information
2 - Simulation Level 01
3 - Simulation Level 05 (incomplete)
4 - Simulation Level 10 (N/A)
5 - Simulation Level 15 (incomplete)
6 - Simulation Level 20 (N/A)
7 - Simulation Level 30 (N/A)
8 - Simulation Level 35 (N/A)
9 - Simulation Level 40 (N/A)
10 - Simulation Level 45 (N/A)
11 - Simulation Level 50 (N/A)
12 - Real Battle Phase 1 (N/A)
13 - Real Battle Phase 2 (N/A)
Medaling in RFJ
Airborne medals can be combined with any medal to become higher-value medals, starting from a value of 100 to a value of 2048000 (which gives a special sound when made, and looks purple, blinging, and gold.)
To get the airborne medals to stick around and follow you, you have to have at least one Slave active, or graze. Since the latter isn't really an option in most cases, it's best to keep only one Slave around or you risk the airborne medal being prematurely collected before it hits the 2 million mark (32 medals collected). A special formation such as Forward may also prevent you from obtaining the medals until you destroy the slaves, so be careful.
After the 2048000 point medal is collected, 9 100-point medals have to be exposed (combining them will "destroy" the 100-point medals, so be careful) to enable the special medal mode.
The special medal mode will drastically increase your rank in RFJ. The medal value is increased Garegga style (10000 to 100000 in 10000 point steps), but without the possibility of recovering their value.
If you drop a medal in the special medal mode, the value for the next medal(s) that appear will go back down to 10000 and you will have to build the medal chain again.
A good run involving only Medaling and surviving can recieve anywhere between 65 to 80 million points by the end of Real Battle Phase 2, so new players might want to aim for this goal.
Rank in RFJ (section info by ycw)
It is largely dependent on power and medals collected. The rank immedately shoots up once you reach these power levels:
Normal Ships:
Power 4 (out of 5)
Slave/Fairy/Miclus:
Power 4 (out of 5)
Guest Ships:
Main Weapon Power 4 + Subweapon Power 4 (out of 5 each)
Basically there's no real way to avoid this, so put up with it.
Medals slightly increase rank per medal collected. In X-MEDAL mode, medals substantially increase rank per medal collected, so there is no hope of you ever having a low rank level once you enable special medals and collect them.
You can reduce rank for a short time if you suicide both slaves in the JP/XBOX 360 version, or suicide one slave in the US/Asia versions.
Dying will drastically reduce rank, but it's bad for score as you'll see later in this post.
Extends
There are none in the PCB or on the Arcade/lower difficulties of the Aces port, but extends are granted in the Aces-exclusive looping difficulty settings Hard (2 loops) and Very Hard (16? loops) at the end of each loop.
Formation Sum
After you have collected two Slave pods and still have 2 Slaves active, collecting an extra Slave pod will change what your slaves do when you deploy the charge attack (or if you're playing a ship without one, this is always active) depending on your Lives + Bombs.
Example:
0 Lives + 7 Bombs = Formation Sum 7
1 Life + 3 Bombs = Formation Sum 4
The easier (harder to some) way to think of this is that the formation sum is judged by a MOD 4 system. but we'll use real numbers anyway to make things simpler.
Formation Sum Effects
For normal ships, these are active when the charge attack is unleashed.
For guest and secret ships, these are active all the time.
0, 4, 8 [Forward]
Forward 2-way Spray, slaves stick out 30 degrees left and right in front of you
1, 5, 9 [Hold/Shadow]
Laser Hold (charge), Laser Snake (no charge)
For those without a charge attack, this can be used as a shield by pressing against the edge of the playing area. Good for 8 hits, replenishes slowly if slaves aren't hit for a while.
2, 6 [Sweep]
Side-To-Side Super-Wide 3-Way Spray, slaves stick a little way behind you going side to side
3, 7 [Tracking]
"Smart" (Stupid) Tracking Formation where they always charge into enemies, never useful unless you want the slaves gone for whatever reason
Bonus Message Chaining System
You might notice some X2/X3/Xn multipliers on some bonuses you achieve. RFJ actually employs a sort of chaining system that depends on the number of special messages you activate on screen. Each consecutive message you activate adds 1 to your bonus multiplier to a max of 9, and 3 messages are displayed at a time (though this doesn't really mean anything to the actual multiplier, but is really the length of time the chain can max out at). The chain is broken when the last message completely disappears.
Collectable bonuses like Fairies or destroyed Miclii are worth one message more but still aren't worth more than x9.
Example:
DESTROYED AT A TIME! (100000x1)
DESTROYED AT A TIME! (100000x2)
QUICK SHOT! (50000x3)
QUICK SHOT! (50000x4)
(messages disappear)
DISCOVERED THE FAIRY! (0x1)
(collected fairy while this message is still on screen, 100000x2)
(or, waited until fairy throws bomb (message disappears exactly when the fairy does this) then collected, 100000x1)
Killing fairies also adds 1 to your multiplier, but you may lose technical point counter, so do this only if you know your bonus chain will benefit more than your stage score.
End of Stage Bonus Tabulation (section info by ycw)
The end of stage bonus is as follows:
ABILITY SCORE * MEDALS COLLECTED * TECHNICAL SCORE
The most apparent modifier to the end of stage bonus is the amount of medals you have collected in a stage, but it may seem unclear what the Ability Score and Technical Score counters mean. Some data is currently missing, but here's what's been discovered:
Ability Score (work in progress)
Generally, the value of any enemy you kill and the BASE value (not post-combo) of any event bonus you trigger, divided by 500 is your ability score. Collecting or destroying fairies does not influence this value. There's a further modifier depending on your stage number, but it is currently unclear.
Technical Score
Not dying in a stage: +5
Destroying over 80% of targets in a stage: +3 (apparently not awarded after you continued)
Destroying over 50% of targets in a stage: +2 (apparently not awarded after you continued)
Destroying over 20% of targets in a stage: +1 (apparently not awarded after you continued)
Collecting over 80% of discovered fairies: +1 (must be at least 1 discovered+collected)
Destroying over 80% of discovered miclus:: +1 (must be at least 1 discovered+collected)
Depending on your medal count and ability score, a loss of a technical point could be a loss of a million points. If you are adopting tactics such as fairy killing in stage 45, remember to be sure that you've collected all the other fairies and make sure you do it in a stage that has at least 5 fairies available.
Not all stages have Fairies and Miclus available, so here's a chart of the maximum technical score you can obtain in the stages:
Simulation Level 01: 10 (3 Fairies / 1 Miclus)
Simulation Level 05: 10 (6 Fairies / 3 Miclii)
Simulation Level 10: 9 (No Fairies / 1 Miclus)
Simulation Level 15: 10 (7 Fairies / 3 Miclii)
Simulation Level 20: 9 (2 Fairies / no Miclus)
Simulation Level 30: 8 (No Fairies / no Miclus)
Simulation Level 35: 9 (1 Fairy / no Miclus)
Simulation Level 40: 8 (No Fairies / no Miclus)
Simulation Level 45: 10 (6 Fairies / 3 Miclus)
Simulation Level 50: 9 (5 or 6 Fairies / no Miclus) (The fourth tank/sixth Fairy's condition is not clear.)
Real Battle 2 (looping versions/difficulties only): (13(!) Fairies / 3 Miclus)
(It is not score efficient to uncover all of the Fairies, though, as a good Quick Shot / Destroyed at a Time chain along with fairy collection may be worth more.)
Ship Selecting
There are only 3 ships worth using: Slave, Ixion, and Judge Spear. This is due to their speed and weapon power, which is required to perform chains more easily.
Ixion's laser attack is the strongest in raw damage, though it doesn't have the special "always on" slave formations. The missile attack is piss, avoid.
Judge Spear is the fastest ship and has the 2nd most damaging bomb and 2nd largest bomb radius (winner of those categories goes to the Raiden Mk2 and Mk2B respectively) but with a slight bomb delay. The weapons are piss weak in comparison to the other two and have to be individually upgraded (L upgrades machine guns, M upgrades missiles), though.
The Slave is a tiny ship with a powerful generic weapon that doesn't need L/M maintenance. It has the same bomb and speed of the ship you select with this. To use a Slave (or Fairy if you choose Miclus) hold Bomb after inserting credit, press Start, then release Bomb.
For those using the PCBs, the Ixion has to be available for the Slave/Fairy to be selected.
For those playing the Xbox 360 port, selecting a Slave/Fairy is as simple as holding Bomb before selecting a fighter.
Hit Boxes
Thanks ycw!

Red areas are the grazing hitboxes, yellow areas are the collision hitboxes.
Stage Paths
more concrete info by ycw from this post:
Sim 01 moves to Sim 05
Sim 05 moves to Sim 10 if you lose two lives throughout Sim 01 and Sim 05
Sim 05 moves to Sim 15 otherwise
Sim 10 moves to Sim 30 if you have not died in Sim 10
Sim 10 moves to Sim 20 otherwise (impossible on default settings if you don't continue)
Sim 15 moves to Sim 30 if you have not died in Sim 15
Sim 15 moves to Sim 20 otherwise
Sim 20 moves to Sim 30 if you have used a continue
Sim 20 moves to Sim 40 if:
-you destroyed more than 98% of enemies
-AND collected more than 90% of medals
Sim 20 moves to Sim 35 otherwise
Sim 30 moves to Sim 45 if you have no missed all stages reached including Sim 30
Sim 30 moves to Sim 40 if otherwise
Sim 35 ends the game (ALL1 condition), or loops in US/Asia
Sim 40 moves to Sim 35 if you've used more than 3 continues (game gives you a funny message?)
Sim 40 moves to Sim 50 if:
-you've used continues but less than or equal to 3
-AND/OR you fail to have the special medal mode
-AND/OR if you have timed out at least one boss
Sim 40 moves to Real Battle otherwise
Sim 45 moves to Sim 50 if:
-you fail to have the special medal mode
-AND/OR you have timed out at least one boss
Sim 45 moves to Real Battle otherwise
Sim 50 ends the game (ALL2 condition), or loops in US/Asia
If you have died at all in Phase 1, you do not get the True Last Boss and you recieve the bad ending (city implied to be nuked). The bad ending gives you a 1 million point end bonus. The stage marker at the end of your score is still marked ALL3.
Otherwise, if you do not die in Phase 1, the end bonus for completing Phase 2 as well as the True Last Boss is 10 million.
Continuing in Real Battle prevents you from seeing the True Last Boss.
In the US/Asia version and Aces Hard/Very Hard, should you die in Phase 1, you just get a truncated Phase 2 without TLB as well as the loop upon completion. The above two conditions and bonuses still apply in the loop.
Further loops, however, will count deaths in previous loops. For example, if you have died once in the first loop and completed it, and died again in Sim 05, the game will send you to Sim 10.
Non-Stage Specific Fairy Retrieval

The red line is roughly in between the start of the last third and last fourth of the screen.
If you destroy the tank turret after it touches it you don't get the fairy.
The tank will still shoot at you if you're not on top of it, and most of the tank auxiliary guns are brutal, so be careful.
Regional Differences
Japan
(Need more info on rank cap/speed)
-requires BOTH slaves to be suicided to reduce rank temporarily
-2 seconds to reveal a Miclus
-one loop, with an Expert Course unlocked with a one-credit ALL3
US
(Need more info on rank cap/speed)
-requires one slave to be suicided for temporary rank decrease
-0.3 seconds to reveal a Miclus
-two loops, second loop has really slow suicide bullets
Asia
(Need more info on rank cap/speed)
-requires one slave to be suicided for temporary rank decrease
-2 seconds to reveal a Miclus
-two loops, second loop has really slow suicide bullets
The Xbox 360 Aces port is identical to the Japanese region for Normal and Arcade difficulties.
shit that doesn't fit anywhere else
- Point blanking deals about 25% to 50% more damage for most of your weapons, and 25% more damage as Slave.
-- Raiden MkII cannot point blank.
useful linx
http://rf-emporium.ghegs.com/ - HI
http://youtube.com/watch?v=hWsU9Emfz6Y - My false start reel where I suicide then restart or just restart if I make a single mistake. Comedy deaths in sim 05!
http://ddp.doorsclosing.com/movies/rfj_st/ - Development folder for this thread
http://www2c.biglobe.ne.jp/~abfuku/raiden/rf_index.html - A.B. DAYO's Raiden Freaks guide, for anyone who can read Japanese
thanks to
Seibu Kaihatsu - for making their last game their greatest
Insanity Naked Hunter - specifically NER, as his game vids were great
Alamone - tipzz on irc
Alluro - tipzz on youtube and a great video showing the boss fight patterns
A.B. DAYO - Helpful stage maps, and the route guide. Wish I could read Japanese so I can make sense of his (much more detailed) stage guides.
incognoscente - correct technical score information
Icarus - allowing me to nick his stuff for the guide, tipzz
ycw - chasing the 2-ALL3, INH hitbox scans, PCB rank, stage paths, score tabulation, and various other info
I am taking contributions and will credit accordingly. Your name will have bolded color in the section you contributed to and you'll feel great* for contributing.
* - not guaranteed, may feel the exact opposite, proceed with caution