I'm not saying it is this or not, but the problem here is that it's not something that can physically be seen ie timing marks. The timing marks and cam lobes will all look correct. It's the relationship between one cylinder firing and the other and the amount of turns on the crank getting from one to another. So if the cams are out and someone does not turn the crank the right number of degrees whether starting from the front or rear it can end up looking correct but wrong.If the cam timing was out, he would have noticed it on the first ride out of the shop and it would have been corrected.
Don't rule out an over-oiled airfilter though as this is an easy fix. Stick a standard one in and it will run much better. A k&N will only give you tuning grief with these bikes. And no sticking a dyno jet kit in wont help. It takes a bit more than a different needle profile and sticking bigger mains in. Even if once you have spent a small fortune of dyno runs trying to get thing right you will have only gained a few extra BHP on top with a standard engine. It really isn't worth it.