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

Thanks again to EVERYONE who has helped me with your knowledge and expertise over the last few years, especially lately! I posted a while back about a misfire immediately after my out of frame overhaul on this 5EK, which turned out to be a timing calibration issue since the engine was entirely disassembled. SO....started working this new engine right away, hauling heavy loads of rock in and out of Wyoming, and really the engine has ultimately been fine.....even after 15k miles of hauling. The PROBLEM....is that prior to overhauling this engine it has a slight misfire, like one cylinder isn't quite doing its job. It's what led me to overhaul it in the first place, with 1.2million since last being apart. I noticed even after getting the BIG misfire (timing calibration) corrected, it STILL has this miss.....even after breaking it in. Under load in low range, starting out loaded heavy, it is a cab shaker. Here's the breakdown....Idle is glassy smooth in the mornings, when things are cold, but the misfire is worse when under load. When the engine is hot, the misfire is worst at idle to 1300rpm, listening to the exhaust it sounds terrible...an obvious "lope" like a hotrod with a hot cam. However when the engine is hot, it smoothes out under load in the higher gears. I have replaced all sensors on this engine, replaced the injector wire harness (again), the engine wire harness is brand new when I out of framed.
The only three things I have not replaced: cam sensor, ECM, and camshaft/rockers......although the machine shop looked at these and said they were good, and repolished the cam. The cam did not have any signs of flaking/wear that I could see either.
1. Can the cam be worn enough to cause a partial miss, without any obvious signs of wear?
2. Can an ECM cause a single cylinder to partially misfire?
Cat ET shows it is cylinder 3...it contributes very little but still passes the automated cutout tests. I have replaced the injector in cylinder 3 (3) times. Miss was terrible with two Cat Reman injectors, but finally smoothed out under load when hot with a BRAND NEW cat injector. Like whatever is causing this problem, the NEW injector responded to it under load much better.....I have yet to read or hear about ECM problems causing this...they seem to just cause an engine to die and no start when they do go bad?
THANK YOU again to anyone willing to chime in on this EXPENSIVE and perplexing issue....

 

I will have to check with the machine shop to see if they mic'd the cam, they said it was ok, but I wasn't provided any specs as to HOW the cam is "OK"....so that does raise the question about this cam. It had been inframed once before, unknown if the cam was replaced at that time, but I'll just assume it hasn't. That being said, the cam just may well have in the neighborhood of 2.5 million miles on it....since that's what the truck has overall. I'm the 2nd owner, the first owner put 2.2 million on it....although just going off of what the machine shop said, "if it doesn't have obvious wear its good." When you're talking precision and wear, that ultimately doesn't count for much. I mean, eyeballing it? Now that I think about it, it's hard not to just pull the cam and replace it since I've done quite literally everything else to this engine. I've been going back and forth about the cam/ecm and with either getting the rockers re-bushed/re-roller'd or remans, cam/ecm are about the same price when you talk about totality of the job price-wise. It's been a relatively slow start to the year and it's just hard to throw a couple grand at a cam and not have it be the problem. I'm wondering if there is a way to test the ECM or injector pulse just to rule that out? Without losing days of work sending it out to be tested?

 

I replaced all the lines on the engine with Cat OEM ones, all fuel/air/coolant, etc along with brand new pump/regulator/primer, I'll check the return line to the tanks, I replaced the fuel return line from the back of the head to the fuel block, but not the line to the tanks. I am thinking how silly it is not to just replace the cam sensor, considering how all other sensors are new. I'll replace it this next weekend or if a work day gets over early. I can check with Cat Tech on the phone but do you know if I have to recalibrate if I replace the sensor?