Ok, been doing more debugging on this pedal and checking the board for problems again, and still can't figure it out. I'm probably going to build a new board, and connect it to the existing wiring. But, I still want to figure out what went wrong with this.
What I've figured out is the following:
1. When I check the pots, there is continuity between the tone pot - volume pot - output switch - output jack. Also, from input jack - gain pot - board.
2. At the board there seems to be no connection between gain pot and tone pot, meaning there is no connection from input to output on the board, but I can't find where/how.
If anyone has any suggestions as to where to look and what to look for that could be the problem I would really appreciate it. Sorry for not posting pictures, my camera broke and have to get a new one.