Thanks to everyone for all the great suggestions. You guys have been a great help, much appreciated.
The heads were bought from Shady Dell Speed, Stage 2 Ported. It is standard procedure for Ryan to go over all the valve guide clearances. That is a well known issue with Eddie heads. I have a lot of faith he did the job correctly. His reputation is second to none.
I agree with Crackedback's opinion about what was happening. When I tear it down after Christmas there should be strong evidence the push rod was being forced out of the rocker adjuster and/or lifter seat. That was a pretty loud noise so marks should exist. The push rod is also a harder metal then the head so there should be some significant marks inside the push rod holes. One push rod has a really big rub mark on it so I believe that is the one that was making all the noise. I would say 12 or more of the push rods did not hit at all. I plan to pull both heads and increase push rod clearance where needed. Some might not rub at idle but could at high RPM which could cause serious problems later. The lifters all need to be removed and carefully looked over too. A lot more checking needs to be done to make sure when this engine goes back together the problem is solved.