I have the exact same problem. Changed plugs and wires, and it helped for about a week, don't know why it came back. I've done fuel filter, new air filter, cleaned MAF, changed trans. fluid and filter, changed fluid in the rearend, new idler and tensioner pully, and took the TB off and cleaned the **** out of it. Next is to test the coilpack I guess.
I do recommend cleaning the TB though, it's really a huge difference that you can definately feel. Just runs so much smoother.