So I went and removed and re soldered all the caps on the power supply board. No change in the distortion. Then I went to do the same thing to the tone board and I noticed an error from when I recapped before.
The CE11 cap was put in the wrong place! (see pics). I moved it into the correct position and removed and re soldered all the caps just to make sure. When it was plugged back in, the popping and scratching was gone!
Everything is sounding much better, however the signal is now weak. I have to crank the volume to hear (see video).
I also noticed that the new CE11 cap that was in the wrong place looks like it's bulging at the top. Does it look that way to anyone else? Could it have been damaged being in the wrong place on the board?