I got the car all back together and ready to go. Problem is, when I try to start it, it runs for about 5 seconds and shuts down. It's nice and smooth for those 5 seconds, but it just cuts out. My logger is showing a code for a CAS. So I just ordered a new one. I noticed when I had the motor apart the plastic housing for that thing was cracked and there was "movement" - so I wasn't surprised when that was the code that popped up.
So, needless to say, I haven't been able to run the car long enough to see if I've fixed my problem. Still TBD.
Bogus - to address a few things you discussed. I replaced the CTS, gauge sender, and rad cap before I ever even posted the thread up. So I already had eliminated those possibilities and was on to the thermostat - which also ended up not being the the problem. Short of doing an overnight pressure test, which I did not do, I'm not sure what else I would have done different. Even if I did a pressure test and lost pressure (which I'm sure it would have) it may not have necessarily helped me pinpoint the location of my problem. I have to disagree with you - I don't think anything I did was unnecessary. I've got somewhere north of $800 into machining of the head - I was very concerned about it being warped or cracked. So sending it off for a level check and pressure test gives me peace of mind knowing I explored all possibilities. I will say good thought on the tune - although my last tune was pretty extensive and only done 2 years ago. I haven't changed anything since then and the car has probably only seen 2000 milies since the tune. I highly doubt tune is the issue, but it'd be something to explore if I continue to have this issue after the fact, along with a pressure test.
MY THEORY - As lazylaser mentioned I really think I was starting to get air in the system and thus cavitation. The right hand side (drivers) of my HG did not have a good impression on it like the rest of the gasket did. I believe b/c the motor overheated the season before when the rad cap went bad I got some head scrub, and, because I don't drive the car a whole lot the aftermath of that incident didn't catch up with me till end of this season. Hopefully in a few days we'll see.
Oh, and thanks for the compliments on the clean up. I didn't have anything else to do while everything was out being checked ... so why not clean.