Jon,
One of our guys just went through a very similar problem. If you've ruled out all the externals in fuel and electrical, it might be internal. His turned out to be a broken inner valve spring. My other thought was a lifter issue but they found the broken spring when they disassembled.
Here's his synopsis:
We changed fuel injectors, wires, plugs, cap, rotor, ECU, AFM. We swapped the injector wires and metered them. We metered the crank sensors, temperature sensors and spark plug wires. We ran a leak-down test and a compression test. Then at the track on Saturday Charles lent us a ECU and we tried swapping it again. We had Jerry and Tim Whitteridge over there trying to figure it out. We then did a running compression test. I had never done one of these before. My compression tester is old and we blew out the Schrader valves. Ron at AIM got us back up and running and we found that the Number 3 was different than the rest. We suspected mechanical failure in this cylinder. No one would believe that the symptoms we were experiencing were mechanical (except Jim Foxx). Everyone thought it must be either electrical or fuel related. (Our team certainly agreed that this was the most likely scenario. That is, of course, why we went through all the above diagnosis.) Our team concluded that it must be that either a lifter had gone bad or we agreed with Jim that it might be a broken inner valve spring.
Previous to Laguna Seca, the car would start fine and idle fine. Goose the engine and it would only run on 3 cylinders. The Number 3 cylinder would not run. Get the car out on track and the car would again run on 4 cylinders and seem to race fine. On Saturday at Laguna Seca, the car would idle fine, but then only run on 4 cylinders between 4500 RPM and 5600 RPM. Very hard to get a good lap in! Still, I was able to qualify at a 1:50.3. On Sunday, the car was worse. It no longer idled and it had a tapping sound. I ran the same lap times. All this made for a very frustrating weekend.
The car was hauled to the team mechanic, Art at Autopoint in Point Richmond. Art went through all the above diagnosis and finally took off the cam box. He replaced a lifter and a broken inner valve spring on the intake of the #3. The lifter was suspect, but the valve spring was conclusive