About the trophies, I think japaese EBOOT searches for japanese trophies and finds nothing (as there are english in folder) and skips them. Replacing english trophy dir (NPWR02193_00) with japanese (NPWR01231_00) should do the trick.
I'm also 2-3 hours in the game, no glitches/bugs so far.
If someone encounters them, you can use vaneilla japanese version to bypass the bug, save and then revert to the patched version
EDIT: Replacing TROPHYDIR really works!