I'll bet anything it's the timing. When I replaced my CCT I was so confident I had tied the timing chain tightly with a cable tie that I didn't even check after changing it out, to see if the timing was right. That was a mistake. The bike started and ran OK but when it warmed up it wouldn't idle. I kept telling myself there was no way the timing chain had slipped, but after checking everything else under the sun, I figured I'd waste a little time and check it even though I *knew* it wasn't going to be off. Well, it was. Check it.
I did the same thing and mine was off the exact same amount. When the CCT is tightened up the bottom crank sprocket WANTS to skip a tooth without letting you know.
I would bet my dollar the timing is off. It is so easy to skip a tooth if you don't DOUBLE check the alignment marks AFTER turning the engine a couple times by hand.
My bike ran good, idled just slightly off and hanged a bit low around 1000, the big thing was just a noticeable power loss in the midrange and it did not want to power wheel in 1st gear anymore. The top end power was still mostly there.