ruff, suggestions?

[TRENDZ]

This may get a bit long winded, but I want to be clear on whats going on here with my truck. I swapped my 90 ctd for an early 91, because I wanted a dually, and my 90 had severe rust issues. The 90 I traded away had an unmolested low mileage engine when I got it, and I put close to 100,000 on it before I went and traded it away, so I know how these things are supposed to run. I knew that the new truck had an engine problem before I did the trade, so it was no suprise to me that it runs as rough as it did/does. After bringing it home, I put an infrared thermometer on the exhaust, and found #3 cylinder cold/dead. I pulled the valve cover and found a bent and out of place push rod(exhaust). I wanted to see what throwing a new pushrod in would do, so I did that. It ran better but not as smooth as I expected. Still, no big deal. I was planing on totally going through this truck. I pulled it down to the frame rails, re-cabed it, repaired all the sheetmetal, paint, new stainless brake lines, new brakes, rebuilt suspension, added an O/D trans, converter, new radiator, reworked interior,etc,etc.... You get the picture. While I could get at it easily, I had the head redone(new valves, guide work, resurface, minor port work), put new injectors (factory non intercooled rebuilt), did the kdp, put in a new rear main seal. While the head was off, I checked companion cylinders for matching TDCs(in case a rod was bent) I still had no idea why the pushrod was bent. I checked camshaft lift also. While the head was out, I put in a 3200 spring, and a piston lift pump.
By the way, this truck was sitting for a few years, the fuel lines were junk, and those were replaced, along with removing and cleaning the fuel tank.
Now... the truck has never run smooth. I've been driving it for about a year as it is. The infrared thermometer shows three cylinders cooler than the other three. Those three are weaker than the other three when cracking the lines, none of them are dead. I suspected a broken cam plate spring, but most of the folks I've talked to that have had broken springs dont describe the same issues I have. The three cylinders that seem weak are on one half of the pump(back side if I remember correctly). I also have tried a 1/8" timing bump.
My next thought was delivery valves. I really never had a dv fail, so I don't know what symtoms would be. Lastly, I suppose I could have got a bad set of injectors, but the pump shop I got them from is known for good work.
I am now in a position where the pump needs to be removed for regasketing the tappet cover. Is there any tests you guys would suggest doing before taking the pump out? I really do not want to do this more than once. Thanks

[1992gen1_fan]

You could fill the filter with a good cleaner and lube, let the engine run a few minutes and let it soak in the fuel system over nite. That might help condition the seals in the IP. Also you could get the injectors re-checked, they'll usually do it for free if you pull them. While the injectors are out, do a compression test.