Regalman,
How did you check the fuel pump, you hooked up a pressure gauge to the schrader valve and pressure was ok? Or did you just disconnect the fuel line at the filter turn the key on to cycle the pump a few times? If you have to mash the accelerator to get it to sputter to start (which is putting the ECM in flood mode) it's fuel delivery. Your pump, relay could be intermittently going bad. On the fuel side you could also look at injectors, make sure they're firing and firing correctly. A bad pulse width / non-fire would cause the same issue. Also look at the regulator, perhaps the diaphragm is bad or you got a crack in the line.
A temp sensor is possilble but you'd be smelling raw fuel constantly and it would run o.k. at first then would crap out.
Have you checked your coil packs for cracks / breaks? Had one on my 3.1L go bad and it run like crap. Would run great when cold, then would misfire when warm hot because the crack opened up, also causing the voltage to short to ground.
Depending on the code reader it should tell you which cylinder has the misfire as Joeyg said - if so pull that plug / wire and check it. If it's plug(s) and wires check out & a multi-cylinder misfire it is probably the crank position sensor.
Good luck man.