You are going to have to get better at reading the schematics! 

Agree, you need to study the schematics properly before making changes, otherwise you introduce more problems.
Print out the schematics, sit down while your watching TV at night and study through them, write notes on the printout to prompt you to look at certain things on the machine.
Learn to spot what looks original and what looks like it has been modified
Generally if something has been modified, it either looks dodgy or different to the rest of the wiring.
Hacks are usually done with whatever materials are handy for the person doing them, that makes them stand out.