Need serious help! Bridge installation content...

[dmc777]

So I parted out my 80's MIJ Squier that had the system 1 trem and kept the body cause it was cracked real bad and planned on making a reliced 60s partscaster and install a vintage trem.

Well, I ordered vintage trem with 2 3/16 spacing, installed it, and the damn thing is off center. Not by much, but enough to where I'm going to have to redo it. The high e "little e string" is right on the edge of the fretboard. Also, it seems like the aftermarket neck I have sits way too high in the neck pocket but I'll get to that later. I'm pretty sure it needs a new nut as well. Good news is I got the scale length correct just the bridge is a tad off to the left and maybe a little slanted.

What can I do to re-install the bridge? Obiviously I'm going to have to take it off but what should I use to fill the old holes so I can drill 6 more hole? I'm using stewmacs template btw...didn't help much apparently. Also, is it possible to get the stud inserts out of the body from where the system 1 trem went? If so, what should I fill it with, and if not, what should I fill it with? Any help would be appreciated. I'll try to get some pics if I can. Thanks guys!