First off, congrats on undertaking such a build! I'm not quite crazy enough to do that, myself.
I read through most of the thread, and was surprised that I didn't see this suggestion. When my Legacy was plagued with misfires, albeit mostly when it was really humid or raining, I did the same thing replacing plugs and checking the coil pack (only one on the non-turbo car). With those dealt with, the problem actually ended up being the plug wires. Something simple we don't often think about, but with that many miles, it would've been worth doing anyway. From what you'd said, you had bad compression / rings as well, but wires would've been a cheap thing to try in the beginning too.