I genuinely don't know if this will actually help anyone, because so many seem to be scrolling right over the explanations that already exist or in some cases are posted right before you ask, but techno is porting the game over to the MV version. It's being done in stages, and very little beyond the basic systems and characters have been ported over initially. The red X's are to keep you out of areas that aren't there, and some of the syntax errors you're seeing are because events in the game are asking for files that haven't been ported yet.
If you want to play the game that has the most stuff in it, download the one that is not MV. Otherwise just wait for more stuff to get put into the MV version.