After sealing all the o-rings with grease and sealing the HSN and backplate the tune was much more consistent. Although every couple of laps there would be a big exhaust cloud and the engine would be down on power for a small section of the track. But this was every couple of laps or so.
The engine is running great so far, other than those issues. The temps I was getting were 210 after 7-8 of race pace driving--with no mistakes actually. And I'd just check the temps when I'd pull in to refuel.
So overall it just sounds like I have some of the "bad" o-rings and I need to get new ones coming but for this weekend the o-ring grease will have to do the trick.