After new plugs and wires, air filter, fuel filter and a good cleaning of the IAC, MAF and throttle body it seems that it was the fuel pressure regulator. No complaints, it needed a good tune-up anyway.
Right after I last posted I had some issues starting and it threw a P0108 code (MAP sensor High Circuit if I remember correctly). There was an air hose leading to the top of the engine at the back side that had been blown off by air building up when the car wouldn't start. I cleared the code and it'* only happened one other time (before replacing the fuel pressure regulator, but with no code being thrown), what is that hose and why would air pressure build up enough to pop a hose off?
As an aside, my transmission fluid was about a pint low about 7000 miles ago, and it was about a pint low again when I checked it this weekend. Could this be a common issue that others have seen?