At least once you have performed the dynamic timing, that rules that out as a problem or if you're very lucky will cure the problem!
The problem with sticking a whole load of parts together from various sources, is that you will invariably need the help of a skilled tuner such as Steve Debben with a dyno. I know the pitfalls of tuning but I'm not a tuner myself. Steve is a member of this club/forum. He is very helpful with advice. I am sure that he would be happy to help. He gave me some very usefull advice when I was building my engine. His web site is
http://www.debben.co.uk/
I suspect that even if you get it running smothly you will benefit from a dyno session to get the best out of your investment.
Sounds like your bike will go like split shit when it is set up!
Make sure you post some pics!
Good luck
Ralph Ferrand
Z1000A1 (1977), Z1300A5 (1983), Z900A4 (1976) GPZ1100 Unitrak (1983)(project), RD250B (1975)(project), ZRX1200R (2005) DT175MX (1981) YZF R6 (1999)
http://www.bikerstoolbox.co.uk