Well, I thought we figured it out...
We changed injectors, then test fired the injectors and coils using the Holley output test. #2 injectors and coil appeared to be firing properly.
We did a compression check, #2 looked good.
I fired up the engine and watched the header tubes with my FLIR. You could see #2 header get hot right away like the other cylinders, then it would shut back off and cool down.
Previous to this, I had swapped #1 and #2 coils, the issue stayed on #2. I had ordered a couple spare Holley Smart Coils, so I went ahead and swapped #2 to one of the new ones.
I fired up the engine and everything appeared to be running properly again. It was running so well that I had to adjust the throttle plate and do a TPS auto set.
We took the truck for a drive, I pulled 3 datalogs.
- The first one is a gentle acceleration from a stop through the gears to about 45mph, then you see me idling at a stop light for a while. This datalog looks good, it's pulling some fuel from the tune, but nothing major, both widebands are tracking close to each other. The 4 lines at the top are target AFR (pink) AFR Right (green) AFR Left (blue) AFR Avg (red) The dark blue line that's hard to see is CL Comp.

- The second one was a WOT pull through 3rd getting on to the freeway. Once again, the datalogs look good.

- We pulled off at the next freeway exit and got stopped at the light. It seemed like the engine was running rough again and it was noticeably missing at idle. We did one more WOT pull merging on to the freeway and datalogged it.

The third datalog shows that we're losing a cylinder on the right side again. It seems like the coil is once again having issues. On restart, the misfire cleared up and all 8 pipes got hot.
We're working on pulling the wiring harness for the coils so we can make sure we don't have any bad connections there (it's still too hot). When we were testing the coil with the output test feature, we were wiggling the wires and couldn't get it to fail. I'm running the Holley Big Wire coil near plug harness but maybe #2 has an intermittent power or ground? I'm not sure and I’m just looking for some ideas.
I ordered the EGT probe kit last week to help troubleshoot, but that won't be here until Tuesday. I'm hoping to get it installed on Wednesday.
Brent