Well, at a first playthrough, I figured out the only real differences in the run are the following:

1. The game seems to run a bit faster and handle the lag just a tiny bit better, but I need a second opinion on that.
2. The acceleration (not the top speed) of the tank on Area 6 is A LOT bigger. It can save a few milliseconds when starting off.
3. You can't suicide in Area 4 when wanting to go to Area 1, you would have to carefully plan your deaths in Area 6 then use the ladder to slowly take 2 health pallets till you die.
4. Some boss death animations are faster.
5. The ending boss death animations is MASSIVELY cut.
6. Left is replaced with Rest (irrelevant)

well, in regards to your first point, i would look into which mapper both version use. If the JP version uses a different/better mapper, it very well could handle lag better. I know Life Force/Salamander is that way, the JP version has significantly less lag, and allows you to have 3 options (US version only allows 2 options), and thats all because it uses a different mapper :)

As far as I can tell the Japanese and US versions use the same mapper (1).

yeah, they do both use the same mapper. its not reflected in this thread, but its now known that the lag difference is due to differences in the way the 2 versions handle their RNG routines.