I was really glad to finally see this thread. Congrats Derek on an excellent job. You have another perfectly restored game in your awesome collection.
I had many of the same issues you ran into. The stencils were great; perfectly detailed and very well made, but they have tons of tiny pieces that in some cases would stay on the backing or front-cover piece. I had to slowly peel the cover pieces straight down too, used a razor blade to remove small pieces, dealt with small areas of paint lifting, touch ups, etc...
I also planned to use the original harness + and adapter, and ended up swapping to the AS harness. I was really glad I did; it's really well put together and labeled so that installing with other parts from AS is super easy.
I have to admit...after using the Ultimarc stick for several months now, the "click-click-click" sound and feel of the stick bothers me. I've actually had it completely apart to see if I could make any improvements. Something about the fact that the magnet centers the stick feels odd. Plus, the restrictor is configured in such a way that moving up/down/left/right is a slightly longer distance in 4 way (when the restrictor is the shape of a diamond) than eight way (restrictor the shape of a square). I'd love to get some sort of solution that uses leaf style switches, but still alows proper 4 & 8 way play.
Anyway, I'm glad I could help out a bit with my previous posts. I got much of the info on my project from the folks here who did Pac restos and multi-jammas before me. I read the entire post on Sypridon's resto at byoac a bunch of times. This project involves a ridiculous amount of work and cost, but it all adds to the personal value and satisfaction each time you look at the game. Beautiful job.
P.S. WHERE is the 720 in your lineup pictures!?!?!?!?