There are a few main differences which impact the run off the top of my head, but the first thing to consider is whether you're playing v1.0 or v1.1 of the JP game - notably in 1.1 the Hunter Transit glitch is harder to execute (I believe it matches the PAL version difficulty of execution) due to the analog control support and this is the most important glitch to perform in the run. I believe Lexichu's run is performed on 1.0.
The next thing would be that JP any% is for Console and Emu, meaning that the Emulator used needs to match original hardware refreshrate & load times - I don't run JP myself so I'll have to defer to the experts on this one for confirmation but I believe the emulator used in NTSC Any% Emulator runs marginally faster than original hardware (I use psx1.13 for NTSC Any% Emu but ePSXe for PAL Any% which is console & Emu because of this difference)
Some other differences that I can recall:
You can't heal after combat without leaving the menu so you need to heal your minions during the earth boss before going into the chosen one fight
Defend reduces damage by ~80% rather than 60% which can give you more opportunities to use specials in boss fights than you have in NTSC
Enemies generally have a smarter AI (will also block) which can change how you execute some fights
I believe the wiki contains a fairly extensive list of the other version differences in case there are other relevent differences I've missed
