Ok... I'm back for an update. Over the past couple weeks I checked the cam timing, which was spot on. Performed a valve adjustment (for the most part the clearances were tight when I got there; I could not fit the feeler gauge in most of the gaps at first so I adjusted them to where the feeler was just able to get in snugly). Today I buttoned everything back up, filled it with oil, and started it up. Timed it to 5 degrees ATDC, and we still had it popping and backfiring around 3 grand. Then I pulled the injectors, and squirted fluid from each one into jars. They all squirted, but one and three were a little low. Three was about 17% lower in volume than the norm, while one was just about 10% down. I wouldn't think that would be cause for alarm, and especially not have anything to do with my backfiring issue; right? Also while I had the airbox off, I had my helper watch to make sure that it wasn't the pop-off valve that was making some of the popping noise, which it was not.
While I appreciate all I am learning by doing this troubleshooting (and it is a lot!), it's frustrating to not find anything clearly "wrong" yet. I'm beginning to think it might have a burned valve...