Join Date: Nov 2008
Location: Morgan Hill, CA, USA
I Ride: Cafe Racer, Commuter, a Dirty one, and a Land Speed Racer.
I did the same thing this past weekend and found the EXACT same results. I started with a vacuum leak and the bike wouldn't run under 3k. Located and fixed the leak, and now it won't run below about 2200 rpms. Anything lower than that and it just falls flat on its face and sputters out. I deglazed the cylinders with my rebuild, so I took mine around the block to see if a bit of break in would help it at all, and it didn't. It's ride-able, until you come to a stop, then it just dies.
My next course of action is to synch the throttle bodies and adjust the throttle position sensor. I'll probably do that this weekend, and I'll keep you updated. You really should synchronize your throttle bodies. When you adjusted the valves, you changed the amount of air that is flowing to each cylinder, so the previous settings aren't going to work as well as they did now that things are different; so you need to correct it for the new conditions.
I would suggest tripple checking for vacuum leaks as well; if you don't see anything, just grab a can of carb clean and make sure.
Setp one: Obtain 5-8 squares of clean, dry toilet paper.
Setp two: some prefer to neatly fold while others prefer the "wad" technique, but you need to condense the squares into a thicker unit of TP.
...do I really need to continue?