I believe that the coils are constant powered and then the ground side is disconnected to create spark. So you might have power at the coils but no spark. The ground would go then to the TCI to activate the spark.
Might I suggest you also put a fitting on the shock mount? When I did my 85 the bolt/pin was worn badly and I had to get a new one made, Yamaha no longer stock those either.
Just a suggestion, but I would advise to let the frame cure for a couple of weeks at least. The paint may feel dry and hard but it will take a bit of time to fully cure. Putting the engine in is going to cause a bit of stress on the new paint.
I also would be interested in what sites you founds the bushings.
Nice job so far, lots of work but will be very satisfying.
Check out the TCI, located under the battery box. Maybe it just the connection being wet or loose, maybe you have internal problems. Do a search on TCI.