unless you know how to program pcsx2 to fix this issue or you can get the devs to fix this (which i doubt as it may take way too much time and may break something else)...
all i can say is this you are running the game a higher resolution than it was made for, so expect bugs like this...
the only other solution is to play with the internal resolution and external resolution to more of a scale of the native resolution like double or triple.... but from my experience it wont work as its not a scaling issue but some special renders become offset as they were told to render at a certain resolution but due to a higher reslolution it shifts to a wrong position...
As for the game looking like crap, well why are you plaing a game for its graphics huh, as far as i can remember the native resolution it still looks better than dmc3 on pc at high res
all i can say is this you are running the game a higher resolution than it was made for, so expect bugs like this...
the only other solution is to play with the internal resolution and external resolution to more of a scale of the native resolution like double or triple.... but from my experience it wont work as its not a scaling issue but some special renders become offset as they were told to render at a certain resolution but due to a higher reslolution it shifts to a wrong position...
As for the game looking like crap, well why are you plaing a game for its graphics huh, as far as i can remember the native resolution it still looks better than dmc3 on pc at high res