Most notably, I seem to have figured out what dictates getting 1UPs from the "random" 100 coin stores, which can have a pretty massive effect on scoring. I'll update this post as I discover the missing details.
How to score:
Avoid getting hit, and don't use your bombs, etc. Pick up excess items when you already have max. Bombs, healing, and shield (if your current shield hasn't taken any damage). The more you pick up, the bigger the bonus you get from this.
Additional lives at the end of game give a big bonus as well.
Getting specific items from stores:
The item positions you see in the roulette that appears after selecting a store correspond to the last digit of your count count.
What item you get depends on the value of that digit at the moment when you activate the store.
When you want to get a specific item try to limit which coins you pick up in order to get the number you want.
At the end of game bonus, each additional life is a guaranteed 50,000 bonus, so ideally you want to go for those on the 100-coin shops, and shield talismans on the 50-coin ones.
If you already have an undamaged shield when getting the talisman from the shop, you still get the (up to 50,000pt) bonus as if you had picked up the item. Conveniently, the 50-coin shops are usually located quite close to a matching pickup.
*) For some reason this doesn't seem to work as intended when you have the max of 999 coins? I need to look into this.
Here's a list of 100-coin stores (that I can recall) each giving a potential 1up:
1: Stage 2, start of stage
2: Stage 2, white snake behind wall
3: Stage 3, after a set of hands before the vertically scrolling section
4: Stage 5. shortly before the 300-coin guaranteed 1up
5: Stage 7, after the bouncing spike balls
Additional secrets or hidden items:
I recorded a video demonstrating every secret in the game (that I know of): https://www.youtube.com/watch?v=9CxxhbAO87E
Stage 1:
- Right before the first cart "miniboss" there's a small island in the water with a hidden chest with healing tea. AFAIK you can only reach this with Ikazuchi and Ame-no-Uzume (??)
- The old guy in the cave right before the midboss will sell you a 1UP if you can grind up 300 coins before that spot (kill ghosts at the start of the stage)
- Right before the bridge, on a pedestal behind a curved wall is a hidden chest with a bomb item
Stage 2:
- Stage 2: Hidden chest with a dog item under the tree right behind the first store at the start of the stage
- Right before the first Rokurokubi building there's a hidden chest with a bomb behind some bamboo on the far left
- Just after that, you can walk above the wall leading into the hallway with several flames jumping around in it, and pick up a barely visible chest with a dog before exiting.
- Right after the three tengu, a white snake can be seen behind a wall. Exit through the wall on the right in the area right above it, this store get can you a 1UP.
- 1UP in a hidden chest behind the destroyed house right after the first fire breathing cyclops
- 1UP from 300-coin shop sitting in a crevice behind some trees near the end of the canyon with the tengu demons (right before the raft). You need to scroll the screen up and then back down to go under the trees. Not strictly hidden, but very easy to miss.
Stage 3:
- Hidden chest with a shield talisman inside the house before the first rock monster
- 1UP in a hidden chest just below the first rock monster (near a different hidden chest in the house which has a barrier powerup)
Stage 4:
- Hidden chest with a bomb on a platform on the right side in the first area with green "bridges".
Stage 5:
- Hidden chest with a bomb item on a completely inconspicious looking platform on the right side on one of the airships
- Right at the start of the horizontal crashing airship ride, there's a hidden chest with healing tea in the upper part
Stage 7:
- 1UP in a hidden chest below a grid ceiling near the jail cells at the start of the stage
- 1UP in a hidden chest in the upper right part of a set of rails where several spiked balls fall through