Ok. I just had two of probably the best mechanics I know looking at it.
Through the process of progressed elimination, we've now got it diagnosed down to the primary intake valve on #3 cylinder. Not sure if it's bent, or maybe a broken valve spring but that's def the problem. So it's nothing Livernois Motorsports did.
Looks like the motor comes back out tomorrow and start ordering a full gasket set. Wee ha! Not bad though, at least I got about an hour on the motor.
When I get it out, one of the guys offered to do a bit more P&P on the heads and relieve the pistons a bit more JIK.