The cipher powerup carry-over is one thing I'm dead certain about, in MD vs AC. In the former, there's no carry-over between stages. In the latter, yeah, it carries over with its remaining energy and you'll want to exhaust it before breaking open a new one. I've been experimenting with getting the new one hidden behind Lago (st4 boss) right before the stage ends in the AC, as (again) the st5 one doesn't always arrive.
I've been looking for some documentation on the item fly-ins but haven't had any luck so far. I wonder if it really is just utterly random. It's not so bad since the flown-in powerups are never necessary, but it sure is nice to know whether they'll appear or not.
Here are the items I know of in the MD port - none of these are in the AC.
stage 1 - walking up the building exterior after killing Strobaya (Ivan Drago knockoff), but before reaching the summit where a bunch of Flying Mosquemen swoop down, you'll notice an "I"-shaped vertical beam overhead. Cling onto its right side and slash through to reveal a lifebar extender. You'll need to jump onto the scaffolding to the right, then take a big somersault to the left to collect it.
stage 2 - immediately after boarding the Sky Thunder mkII (mothership), before you jump over the first turbine, there's a hidden single 1HP restore in the alcove above Hiryu's head where the bomb chutes join the fuselage.
stage 3 - after escaping the crusher trap and killing Mr. Elephant and the Hit Mice (good name for a band, that...), go right, past the uppermost launcher trap. At the very end of the platform there's a hidden lifebar extender, you'll need to jump and slash to reveal it.
stage 4 - trigger the collapsing bridge without crossing it, then climb down the leftmost wall into the water and slash to reveal a hidden lifebar extender.
stage 5 - after killing the Shadowtag Bullet Gunner, that cheapshot motherfucker, climb onto the satellite dish directly above and slash to the left to reveal the MD port's exclusive second extend. The first is in Siberia's power plant - head up the long ramp all the way to the left and kill the Frog mech, it's just behind it next to a lightning generator.
The saucers are absolutely disgraceful in the MD version. :/ The AC's maintain a tight orbit around Hiryu between lashing out and nearby enemies, here they're more likely to wander off somewhere leaving you to fend for yourself. This is like a Gradius port where your options go off and do their own thing... actually, scratch that - they're like the Flint from XEXEX. Easily the worst aspect of this version.
Amusingly, just like the Wii VC version of The Revenge of Shinobi and its dopey redrawn title screen (no Sonny Chiba for you!), its version of Strider MD is censored.
TOO MOSQUE FOR TELEVISON. -_-