ECU was fine. They tested it on a couple different cars, including their big power test mule (over 300whp).
I wasn't going to tell anyone, but let's take a look at what could cause a misfire, ignition-wise. Spark plugs, spark plug wires, coils. I replaced plugs twice, and tried different coils. I changed the last part. Problem gone.
I wasn't going to tell anyone because I felt like a dumbass. The only part that I didn't change (because I figured they don't go bad very quickly) and it was the culprit.
Everything seems to be back together with no issues. Drove up to the Mentor Winking Lizard last night from work, then to home. Round trip of 104 miles. The needle just barely left the F line when I got home. And before anyone says "Oh, the map was your issue all along too, you're getting good mileage!" I have several tanks documented getting the same initial mileage with the old mapS.