Did you use 2 of each gauge to set the valves ? Not necessary, but you will get your best adjustment that way. As for the rough idle, they might have played a part, but probably a small part. How old was/is the gas in the bike ? Seeing as how the bike has been sitting since summer, if it has ethanol in it, it could have water in the fuel. Might want to either drain it, or top it off with new 93 octane fuel. I don't think I would mess with the throttle bodies until you are sure you have good fuel in it. And as for the valves being tight, well, they usually tighten up as your miles go up. Not the end of the world.
1998 R 1100 GS
2007 K 1200 GT