I did a complete rebuild on the motor about 200 miles ago, also added a temp gauge.  The bike runs great but I rode the bike about 20 miles on the highway between 50 and 60 miles an hour.  The temperature never got over 355 degrees but noticed with engine cold it goes to idle but when hot it does hang for a second.  My question: is the motor sucking air when hot and should I be concerned unless it runs hotter?

You could try going in on the air screw 1/2  turn or so or one size up on pilot jet.

Did you source the original dual lip crank seals or did you use the aftermarket seals? 

Anyway, you're probably fine. 

Thanks Mark I did use the correct crank seals from enduronut. I assume as long as the temp doesn't get over about 400 degrees I should not seize the motor.

Ummm....  I would not make that assumption.  CHT is great but if engine goes into detonation/preignition it will lock up way before you see too high a temp on the gauge.  It only takes a couple seconds. 

Have you ruled out any air leaks? Give it a quick pressure check if you haven't already
It's always surprising where the bubbles turn up sometimes.
-- Ray

I did a pressure test after rebuilding but maybe need to do another.