Sounds like its probably the intake plenum gasket. I went through the same thing with mine when I had it years ago. Once that gasket goes bad you basically draw sludge into your vacuum system an it gets deposited into the fuel tank. Which in turn cloggs the fuel injectors causing the misses you're getting.
I changed the gasket, dropped the fuel tank and completely cleaned it and cleaned the injectors and it cleared up all the isues mine was having.
To clean the injectors, hold one in your hand and fill the top of it with rubbing alcohol. Then use two jumper wires from the pins on it to a 12 volt car battery. Never hold 12V to it for more than a second. Just tap the wire on the battery post over and over to flush the alcohol through. You want to run a good bit of alcohol through each one. It'll take a while to flush all the oil out.
