help diagnose problem

[RB92GT]

Ok guys, this is a long one, sorry:

I've been having a strange problem with my '92 GT. It has about 45,000 miles on it and has a T5 tranny. Within the past 6 months, twice the car sounded like it was running on only 7 cylinders, but the problem only lasted a few minutes and then disappered. While cruising along, all of a sudden the car would hesitate a little, and the RPM's would slightly drop. After coming to a complete stop in neutral, it was idling at 500 RPM and was shaking badly. I popped the hood and the engine was shaking all over the place and was emitting a noticable tapping or clunking noise.
I have an electric fuel pressure gauge, vacuum gauge, and oil pressure gauge, all of which were in the normal range.

Within about two minutes, the RPM's would jump back to the 670 range where it should be, and the car ran absolutely great again. I bought a code reader and came up with the following codes:

KOEO (continuous memory):
95 (Fuel pump secondary circuit fault)

KOER:
94 (Air diverter solenoid circuit fault)
44 (Thermactor air system fault)

I have a fuel pump cutoff switch, and have turned the ignition on a few times with the switch off (circuit interrupted) so I think that's why I got a code 95. I removed all my smog crap, resulting in code 44, and maybe 94? What is the air diverter solenoid circuit?

I did a cylinder balance test, and all cylinders are normal. So, after all that, any ideas what the problem could be. After I had the problem the first time, I put a fuel injector cleaner in the fuel. I changed the fuel filter about a year ago, and did a complete tune up with 9mm FMS wires, plugs, distributor cap and rotor. Could it just be crap in the fuel getting caught in an injector?

Thanks,
Ryan