A little late maybe but... I just found out the same problems you have for myself , same re-build, same carbs, i tried a lot of the same things you did but nothing really solved the problems. finally i found some info about 34mm flatslide mikuni on this forum,
The stock needle jet in these carbs are too big. go for a p8 or p6 jet, you will have to rejet it but i'm pretty sure it will run great.
(Im from the netherlands , excuse me for my bad writing)