Ok, a little more info.
I talked to the dealer again that was going to turn this into their warranty department, nothing came of that, but he did give me the contact info of a couple of very reputable shops that specialize in the 6.0/6.4 Ford truck. Neither have seen this and both originally looked towards an install error or some other component way out of spec. Both agreed that the push rods only helped center the plunger in the lifter, and had nothing to do with bottoming completely. After some detailed explanation, neither could point at one thing but both agreed something is odd, which I completely agree with.
So tonight I have both new heads installed, and ran a compression check and a true leak down test (picked up some gauges today). All checked out good with the #8 cyl having a slight leak in the exhaust valve, but still only about 25% loss compared to the others at 20% so pretty close overall. Compression test is about 10psi less than the others. Likely a valve that will seal better after break in.
Now the interesting part: I put my stock push rods in to see if these heads/rockers do the same thing and they do. No, it isn't as bad because they do seal and get full pressure, but I can put 2 blue paper towels between the valve and the rocker and I start to lose pressure. Effectively the lifter is bottomed and the valve is just on the edge of sealing. 3 paper towels and i'm losing 70% of the air. I don't know what 2 blue paper towels come out to when the are compressed, but it can't be more than about .001-.004. What this tells me is that the now second set of heads and rockers have the same issue as the first set, only maybe slightly less. The only other component I did not change that was changed the first time is the lifters. This would tell me that if anyone gets away with swapping heads/rockers without changing push rods (job 1 trucks), is running with the lifters fully compressed.
I've pretty much decided everything is within range with the new shorter push rods so i'm going to start buttoning it up and see what happens.