Good job you're doing there YZman. I found this thread yesterday and thought that with a start date of '09 it would be long finished by now
Life has kind of got it the way, I hope that the future is looking brighter now.
You are probably aware that most of fthe issues with these old BSA 650's were down to axial movement in the crank causing bottom end lubrication problems. You referred to a "shim kit" that you got from Ed the engine man which may be an issue down the road. If you have a roller primary side bearing and a bush timing side the thin shims that BSA used can cause issues and a custom one pice shim in place of a stack of thin ones is considered the simplest way forward. Have you seen this thread?
http://www.piled-arms.com/tech31.html
Apologies in advance if I'm preaching.