3406E misfire that won't go away, even after overhaul

I definitely did not do anything to purge oil from the jakes.....I just set them at the same time I set the exhaust valves to .030. I was very careful, they are pretty touchy. Would that cause the jake plunger to hit the rocker and hold the valves open a bit?

 

Thanks for the procedure Sauer and for everyone's help! No I'm ashamed to admit that I didn't do that process when I ran the overhead.......I'll get right on it tomorrow when I finally have time to put the dial indicator on to measure the cam rise. Between trucking and springtime farm work it's been absolutely nuts. And also, I did not put on tune-up kits on the Jakes, they are the 340A's. I've put another several thousand miles on this thing and the miss is steadily getting worse..... since I had the software taken back to pre lownox, it is also blowing a LOT of black smoke as well, still struggling power-wise.

 

All right, finally an update. Once again, thanks EVERYONE for your time and for your advice, I just have too much invested in this Cat to give up on it just yet. I checked over everything again, ran the overhead again, purged the jakes like I should have the first several times, and hooked up a dial indicator and measured the rise of the rockers as it was barred over. I can't remember exactly what it measured at, but cylinder 3 exhaust and intake was pretty much consistent with the others. As it was an old cam and old rockers, I went ahead and just ordered new ones and dropped another $3k into this thing. First thing I noticed was it was easier to get the overhead "just right" with the new rockers and shafts, and I noticed right away upon starting that the miss was about 25% better than it was, but still there. So that gets me to 5.5 cylinders out of 6 instead of maybe 5.25. I used the 139-0538 cam instead of the 187-9381 stocker, and it did seem to help it want to maybe pull a little harder, but still that miss....... You can really feel the un-evenness of the firing order in the low gears, starting off with heavy load, and boost still hangs out around 30psi at max load, the needle on the gauge just shaking like crazy. I'm running the 170-8132 file, which I'm not sure if it was meant for 57's or 58's injectors...mine has 58's from factory. Checked on both the other trucks, they are 5EK's with 57's that run circles around this one still. Is there something with 58 injectors that I should be considering? Maybe a change back to the stock programming to regain power and maybe help this miss? Next on the list is to back off the jakes clear far to see if they are causing problems, I watched them with the valve covers off and they don't appear to be touching the valve bridges.....

 

Well, checked another thing off the list this last weekend, pulled the 3-4 cylinder Jake unit, went all the way through it, the control, slave and master pistons were free and not seized, pretty much just fell right out. They didn’t show any signs of wear but I replaced everything that came in the tune-up kit, tested the solenoid and it came out within spec, 10.7 ohms. Also re-calibrated the timing and that was successful. Also replaced the cam sensor prior to calibrating. Engine seemed to “want” to make power but still not a good, even engine feel or sound. Still struggling with small loads, sound and feel of this engine running is more of a bubububub instead of that smooth even cat growl that we all know and love. Drawing a blank after all this. Wondering if even though I don’t have any bubbles I can see in the fuel if there is just enough bubbles coming through from cylinder 2 to get sucked in by #3 injector to make cylinder 3 misfire slightly? I read the post about fuel return issues that just got resolved on truck 307’s thread, his was not a steady miss and low power issues though. Still no blow by, not using any oil between changes, just have to floorboard this gutless, uneven wonder even after all the money and work I’ve put into this thing. Just wish I could locate a smoking gun, even if it’s major.

 

Another update.....had hydraulic hoses made with JIC connectors to run fuel supply and return directly to the tank hoping to find a fuel issue, fuel pressure remained the same idling at 85-90 and 105 at 1500rpm. Went for a spin and pulled it up a hill floorboarded and no change in fuel pressure or power, so I guess I can rule that out. I then had FTS/FLS set to what is believed to be a hotter fuel code... 62/-19. LOTS of smoke....I mean pouring out the stack and maybe 3 psi more boost out of this nice 0000 borg turbo. But not an ounce more power to be felt oddly. So I switched to factory fuel numbers, -5/-10 and switched to 170-8227 brakesaver file and it made it a little more snappy but boost is down to like 27-28. I also switched fuel pressure regulator for grins and also no change. Replaced the grounds on the head to the frame and no change. I’m also getting 100% throttle while driving according to cat et. I did see the atmospheric pressure is sitting at 13 constantly? Is that about correct? Trying to look at all the readings to see what may be the culprit because this engine should run great. Fuel temp sits generally at 148-152, wondering if this is too hot?