Main Motorcycle: Thunderbird 1600
Join Date: Mar 2011
Other Motorcycle: Kawasaki z650 chop
Start the bike without touching the throttle. Leave it running until the fan kicks in, then start timing. Once it has run for 12 minutes, I usually give mine a minute or so over to be sure, turn it off.
Start as normal and the bike should have self adjusted. This will get rid of a lot of problems like yours. Not all of them but it's cheap and easy to do.
Cleared up a couple of minor tuning problems in the past, and is probably a good first step if you are having problems.