I approve of altering something so it works for you. I'd have to make changes to it, too.
not really any way to line it up without making the holes bigger or floating the trem. i wouldnt do either so id either put the old cover on or pull the silly thing off and throw it in the case![]()
You can move the vibrato block into alignment with the holes using the vibrato arm.
Fender bullet-end strings make things easier on Strats.