Glad to see someone working on improving this. Hopefully some more stuff I can modify to work in real time D
As for version differences, the J version obviously has drastically faster text. There are also a few minor changes to bosses
Metal Mantis obviously a bit faster because of room layout.
3rd lion statue boss has a bit different AI, so strategy for killing it may not directly transfer over (though first 2 seem to be identical)
Skull boss appears to have less HP, as it can be 2-cycled in real time
Poseidon's room layout is altered with the ledges on either side extended, making it possible to deal damage when it's on the left or right before descending to attack.
There may be another few differences, those are just the ones that come to mind. Don't want you to plan a strat on one version only to have it fail or be suboptimal on the other =)