Eventually it was a hard miss, a dead hole, that was cyl. 8, with a warped exhaust valve. The misfire would come and go, sometimes worse than others. If 3 cyl. were misfiring bad it would shake a bit. The V-10 has a strange firing sequence, some cyl. are 90 degrees apart and some are like 52 degrees. That's why it sounds the way it does, maybe it also smoothed out some of the vibration, dunno.
Vacuum gauge, yes. Vintage 1954 SnapOn. I'd get some movement out of it if the miss was bad, but not like you might see on a V-8 manifold. The volume of the plenum may damp it out.

 

Thanks for the update guys. I did try to bypass of the ICM, which once I followed the wires I found that the ICM actually runs both the 4 and 6 packs, and like 69_XS29L said, didn't work. I'm going to try to convert back to the original coil packs this week to see if that works. At this point I'm willing to pay a shop to find the problem, but the shop we've been using for over a decade couldn't or didn't want to figure it out. If it doesn't work when I switch it back to the stock coil packs, then I might be taking it in to another shop. It seems to misfire at random (not necessarily only when it's warmed up like I though), but once it starts misfiring it will continually misfire until it gets restarted (which luckily it's a manual so I can just push the clutch in and coast while shutting it off and back on and if I flip the key fast enough the engine wont stop spinning completely by the time I turn it back on, thus eliminating the need to use the starter to fire it back up). DUI said that the rise time of the 95' might not be fast enough for the new coil packs. Other than that he's not sure what it is.

 

Good catch and I misspoke, ICM runs 4 of the cylinders, not all on the 4 tower pack.

 

Switched back to the old coil packs, no more misfire. It probably has something to do with the rise time of the coil packs. I'm a little sad I couldn't get the performance ones to work, but it is nice that my dad can now use the truck again. The truck is however back to running how it did before we started this project. There is a slight hesitation or something, when you give it a little bit of gas the rpms drop before they rise. It's easily overcome by giving it more gas, but this gets annoying for precision movements, especially when pulling a trailer where it will nearly stall out. It is a manual transmission. It didn't seem to do this with the upgraded coil packs. Any thoughts? Probably just needs new coil packs.