Frustrated, can anyone help ?

Hey fellas, I did my slide stop kit, velocity stacks, bmc race filter, and ignition advancer a while back. I did it all at once, (me and my friend did the install) Anyhow after the installation the bike ran great with a custom map for the bike, but the bike never held such great idle, it was sputter on cold starts, when warmed up the idle would be high as 2,000 rpm...so i figured eh my throttle body might just be out of sync due to the slide stop kit, so i always put it aside, and the bike rode great, n i didnt have the tool to sync them, so now i figured eh might as well just drop it off to the shop and have them sync them..now the nightmare begins..they cant sync the tb, the bike is running like shit, cylinder 2 is running cold..spark and fuel is good, wut can cause this problem ?? coils are good, new plugs, i dunt know wut else can be the problem any help would be greatful =T