I am sure others will chime in...but, let me beat the dead horse first, and if I have missed a post somewhere stating you have already done the basics, I apologize.
Be sure your vacuum caps and hoses are in good shape. Also, check o-rings under the intakes. They are bad about leaking after a few years. Tighten the clamps on the carbs. If you haven't replaced the o-rings under the intakes, they are not hard. If you have vacuum probs, a sync is a waste of time.
A set of vacuum guages is a must for good synchronization. You haven't ruined anything, just need to start at the baseline #3 carb and go from there. Maintain engine rpms while syncing, proper cooling to keep the fans from coming on etc..
There are some write ups in the tech section of the f6rider board that may help. And of course, the wealth of knowledge and opinions posted here will broaden your sense of knowing and well being!

Maybe someone is close enough to help you out.
Good luck!
Craig
NcGhostrider
99 I/S