Truck Forums - Random Misfire on 99 Sierra 1500

Hello all, I'm hoping I can get some help from the group because a local shop and now the dealer service team have failed to. I apologize for the novel below but this has been kicking my butt for several weeks now.
Over a period of a couple of short drives, my truck went from running perfect to barely running at all. The rough running (like running on 6 cylinders) would start immediately when cranked cold and would never change characteristic regardless of conditions. The computer would only log P0300 "Random Misfire" codes.
After doing all of the normal maintenance items (replace plugs & wires & fuel filter, removing and cleaning throttle body and MAF sensor & KN filter) the problem didn't change at all.
I took it to a local muffler shop to see if the catalytic converter was the culprit and instead they hooked the truck to are larger diagnostic computer that read the spark misses per cylinder and when under very heavy load the #7 would miss heavily and #5 about half as bad. This led me to replacing both of the coils which also had zero impact on the problem.
I took it to the dealer and after $500 of labor they said there was contaminated fuel and they cleaned the fuel rail and injectors. In retrospect I believe the technician ignored the fact that I told them I had a can of sea foam in that tank of gas. I couldn't afford the additional $400 they wanted to drain the tank so I had the truck towed home so I wouldn't suck in potentially bad gas into a clean injection system.
I dropped the tank and fuel looked perfect but I disposed of it and cleaned the tank and refilled and replaced the fuel filter again. When I started the truck it ran perfect for my about 10 mile celebratory ride. It started perfect this morning and after 1 mile I felt the miss come back.
Two potential related side notes here;
1) The bolt has been broken off in the manifold closest to the firewall (#7 cylinder) so I've been listening to that hissing when cold for several months.
2) The fuel pump has been whining for about 2 months and very noticeably wasn’t during my victory drive last night but I heard it again today after the problem came back. I've been told that a pump either does or doesn't work and wouldn't cause this problem but now I'm not confident of that.
Any advice would be greatly appreciated because this truck is fantastic and it's the first mechanical problem I’ve had with for 8 years since I’ve owned it.