Did you sync the carb when you put it back onto the bike? Also sounds like your mixture might be a bit off. Couple of products you might want to look into:
a) CarbTuneII -
http://www.carbtune.com/ - if you pull your carbs, you need to rebalance them off one another so that the vaccume is the same for all.
B) Colortune - the cheapest and easiest way to ensure your mixture is set.
http://www.carbtune.com/colortune.html - you may be able to find a local supplier of that product.
I own both - the cost of buying both items is 1/3 of what a shop will charge you for a simple tune up.