Patrick,
I have reread your post a couple of times and am wondering about a couple of things.
First, was the idle miss so pronounced that it was the motivation for the mechanic to pull the heads off?
I have had, as we all have, cars that had intermittent misses and rarely was it something so serious that I felt the need to have the heads removed. There have been a few times that it was that serious and burnt or sticking valves were the issue.
You said that the miss was in cylinders 5 & 6 which is odd that they are exactly opposite each other and their primary shared connection is cam lobes. You also said that you had replaced plug wires, etc. and I want to understand clearly that this was because you were doing routine maintenance or was it because you were trying to solve the miss?
Now that the heads are off did the mechanic identify any valves that were burnt? If he did not would it be possible to check with the machine shop that performed the work to see what their thoughts were? Did you have them install hardened seats so you can run unleaded with no issues?
Are the heads back on the engine? If not it would be helpful to have them cc'd so you have a base line.
Has your mechanic measured the installed valve stem height? This basically is the height from the spring seat to the top of the valve stem. Most of the better machine shops will do this as part of the rebuild but if he sent them to a production type of shop they may not have checked. This will tell you if the theory of the push rod length being too long is correct.
I am also curious about the pressure check that your mechanic says he performed to test compression. You really only need 40 lbs. or less of pressure to check leak-down depending on what type / brand of gauge you are using. The 100 lbs. he says he used is too much and yes it would build more compression due to the extra pressure on the rings causing them to set a little better, but not an indicator of much of anything else.
Explanation of pressure leak-down test:
http://www.carcraft.com/techarticles/116_0406_cylinder_leakdown_tester/