Just read this thread for the first time. I'm going to go with the suggestion that it's your home-brew porting job. The other mods you've done may add to the problem.
I have a throw away head (hairline crack) and I spent probably a dozen hours or more working over the ports one or 2 at a time and testing them on a flow bench. It was amazing the results I got. Most importantly, it was extremely difficult to get consistent results. In some cases, I improved flow at low valve lift and had it drop of considerabley at high lift. In other cases, just the opposite. And as the flow rate changed, so did the results. The point is, you just can't realistically go in and remove a bunch of metal and expect great performance or mileage unless you're extraordinarily lucky.
Everything else you've checked and double checked, it appears. This is the one thing you can't check. I may be wrong, but from my little bit of experience with porting, that's where I'd say your loss is from, at least a fair amount of it.
FWIW,
-Jay