I got the motor on my '97 put back together after replacing the tranny bearings and shell bearings due to mysterious aluminum flakes found in the oil pickup screen.   The engine internals seem to be good, but the freaking caburation is driving me up a wall.  The carbs came off at the beginning of the rebuild, were put in a plastic container with a lid and weren't touched during the entire process.  The bike is running lean, bogs when the throttle is opened, over revs before settling into an idle.  I had the carbs off today for a cleaning, couldn't find anything wrong, took out the floats and jets and spritzed all the passages with carb cleaner and it didn't change diddly.  The rubber mounts are fine,  no air leaks; gas flow from the tank is not the problem, all the vacuum and overflow hoses are connected correctly.  I'm about an inch away from turning the bike into landfill.  Why would it run lean or bog on accelleration after an engine rebuild?  Is there anything non-carb related that could be the factor?  It can't be timing, since there is one default setting.  Any ideas would be appreciated.

Well, the "over revving before settling into an idle" indicates that there is an air leak - probably around the rubber mounts. Did you get new orings between the carb mounts and head? New carb mounts might help as well, but those orings are cheaper to replace and are prone to leaking.

As far as it bogging when coming onto the throttle, I would say check your float height using the clear tube method.

It does sound like a carb issue, but are you 10000% sure you got the timing 100% correct when you put the cams back in? If you are off by one link the bike will run, but not very well. I think that happened to adidasguy's junior when we made a new engine out of a few different engines. It's been awhile so I don't remember how the bike acted when the timing was off.