So I've recently learned how to set up guitars. Love doing it myself. I aced a few years of college level physics, so (at one point) I understood electricity, resistors, capacitors and all that. I'd need to brush up , but beyond that, what should I focus on, what should I read, to learn about amp modding/building?
Look at this amp building Clinique run by Bruce Egnater www.sweetwater.com/store/detail/AmpClass2/

The class is full right now, but they do them a few times a year and the cost is $2500ish for doing the class and you build your own amp to take home. It is typically a Plexi/800 build
2002 PRS CE22
2013 G&L ASAT Deluxe
2009 Epiphone G-400 (SH-4)
Marshall JCM2000 DSL100
Krank 1980 Jr 20watt
Krank Rev 4x12 (eminence V12)
GFS Greenie/Digitech Bad Monkey
Morley Bad Horsie 2
MXR Smart Gate
Definitly look at ax84.com, lots of good information.
Just start with going through the P1 theory document there, that will explain you the basics and illustrate it by their ax84 amp.