Hey wantahertzdonut:
If it runs better, would you recommend a K&N or just a stock unit?
I only asked them to do a stock tune, they shouldn't have changed any of the jetting
Yea, I agree, it is not likely they changed any of the jetting, but it IS possible that they tweaked the pilot air screws.
That's whey I suggest looking at the air filter first, and look around in the air box, because your symtoms sound a lot like a clogged air filter, causing the bike to run rich. I'm not fully familiar with the 1G 600, but on the 2G, you can get the air filter clogged with oil coming up from the engine vents, so look at the filter and in the air box. As for filter type, the K&N is usually a recommended upgrade for the 1G's (Not the 2G's), but it needs to be clean and not overoilled.
If your still having issues, look at the spark plugs to see if the colour is good (light brown) and that all plugs look similar. If you have some very dark or carbon looking ones, you may be up for a carb removal, cleaning, etc.
As for a manual, search the site, there used to be some links to downloadable manuals here.
Let us know what you find...