#1
Im modding a Squier Affinity Series strat and I have read some reviews on Fender bridges that the holes dont match up on the Squiers. So I was wondering what would be the best bridge to put on the Squier?
#2
Do you want a trem or a fixed bridge?
Be prepared to do some routing, it's not gonna go in easy.

Also, there's no point in trying to upgrade a guitar that's cheap in the first place.
Save up and buy a good one.
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#3
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Also, there's no point in trying to upgrade a guitar that's cheap in the first place.
Save up and buy a good one.

False. It completely depends on why the guitar was cheap in the first place. If it is cheap because of poor construction, lousy neck, bad electronics and pickups, and a plywood body that is then coated in plastic instead of paint (read: low-end Epiphone SG), then it is not worth it.

However, if it was cheap because although constructed fairly well out of decent wood, the frets need some love and the electronics and pickups are bad (read: Squier Affinity Strat... just like TS has, who would have thought?), then it is certainly worth upgrading.
#4
fill the holes with wood & wood glue - let dry and add your new bridge.

but whats wrong with your old bridge? just lock it down & tighten the tremolo screws and throw away the wammy bar.