2005 Chevy 2500HD 6.0 gas misfire

A neighbor of mine asked me to help him with his truck that he now needs for basic transportation.

Done so far: 1. Both front hubs were bad, replaced with new. One fell apart as we took it off the knuckle. 2. Both exhaust manifolds had broken bolts. I welded nuts to 3 to get them out. One broke off so deep I couldn’t get it out, so I was forced to use a manifold clamp to seal the manifold to head. Good news, NO leaks now! bad news, he drove it a good bit with the leaks. 3. PCV line cracked in 2pcs. Purge line had a crack starting and was leaking vacuum. Fixed both. 4. during EVAP troubleshooting, found the FTP sensor was bad. of course the gas cap leaked too, so after replacing both, the EVAP works great. He is lucky he didn’t trash his CATS and O2 sensors.

Good NEWS! the truck runs good, and it passed NC emissions inspection with flying colors. Fuel trims great, CATS and O2 sensors OK. NO engine codes at all. and the drive cycle readied all systems

Bad news. Cyls 1&6 have a random misfire, the count goes up slowly misfires occurring every 3 sec at idle (they were the cyls where the worst exh leaks were located). Does not throw a code for misfire, but does show up on the scan tool count. Since the owner wanted to get his inspection in this morning, I didn’t spend much time on the misfire. You can feel it, but engine performance seems OK and fuel trims as I mentioned great.

If you think I’m missing something please let me know. The owner is on a tight budget, and he is a good guy. I’ve spent a lot of time fixing the urgent stuff with him buying the parts. The two bearings were a painful purchase for him.

My next chance to work on it will come in a week or two. I plan on doing the following:
*Run a relative compression check.
*Use a secondary spark inductive probe to look at Cyls 1$6 and compare to a known good.
* Run a compression test and cylinder blow-down on 1&6, suspecting the exhaust leak damaged a valve. When we had the manifolds off to fix the leaks, all the EXH valve stems looked the same, a light coating of white ash. I looked as best I could with a bore scope and saw nothing remarkable on the manifold side of the valves.