Drew.

If it hovers OK without TBE then I would guess that your hub could be too low. The links will actually hit the motors, especially when you lean the swash plate forward. I would measure the stock outer shaft hole locations and drill locator holes in your carbon fiber shaft. Do the following:

Put your rotor hub on the old stock shaft and tighten the upper locating set screws in the locator holes. Then measure from the top edge of the hub to the top of the shaft. Now place the rotor hub on your CF shaft at the same height. Tighten the top set screws to make marks in the CF. It's trick to get the drill perfectly centered when you drill through the shaft. So I just drill a hole in the middle of the mark on each side rather than trying to run the drill all the way through. Keep the locating holes small because they will weaken the shaft.

Then level the swash plate and you should be good to go.