What do you mean, they don't line up? Color burst should appear after every horizontal sync pulse with fixed amplitude. Then color info of same or no amplitude and variable phase depending on the display. Can you post scope photos sampled at various points in the circuit?
Have you traced the color subcarrier signal from the GTIA all the way through the circuit with a scope, to see where it's getting lost? Is there maybe something in the circuit that limits bandwidth below 3.6 MHz?
No shame at all. Atari made the best possible membrane keyboard, with raised edges for tactile feel and the speaker click which you can feel and hear for feedback. Yes, not good for touch typists, but good enough for entry level in 1979.
Please take that discussion, any more repair notes, and other OT posts, to other threads. Thanks.
Meanwhile, I've updated the sheet linked in the first post.