Well alot of the books on Amazon go for stupid amounts of money, there was a thread on here with some downloadable E books if you can find it, but i'l add a list of the Popular books a bit later.
Regards the theory, the books are pretty good for that sorta stuff, Geofex which is listed in the links has lots of information on it if you search for it, it's difficult to find a begginer level of theory the best way I found was to jump in and start messing about with circuits and then it begins to come to you and then you begin to understand the information that seemed to make no sense before.
The simplest sort of mods that can transfer to alot of things will be changing the type of diodes in a circuit for a different type of clipping (e.g. changing the 1N4148 diodes to 3mm Red LEDs in a Proco Rat will make it louder with a more compressed sound) changing the chips/ transistors in circuits for different ones.
The best thing to do is buy a breadboard, build a circuit and alter all the values and see what differences it makes, you'll learn alot faster doing in electronics than reading i'd say but i'l try and add some info on this sort of reading later.