Could be as small as a weak valve spring, or something along those lines. Gotta deciede if its a big enough issue, and you have the money and time to possibly rip into the engine to fix it. At my current state I have neither available to take on such a task. If your in va I'm sure you could talk to 02tj, he has a scope and thinks he could find the issue.

 

Ok, based off of the OP's first post, it looks like there is little left unchecked. Here are the things I didn't see mentioned, so I wanted to just double check specifics and then add my .02... So apologies if this gets longwinded... And remember this is just for the sake of being methodical, so I'm starting top to bottom..

*note: IMHO/experience, cheaper parts from discount auto stores (online, certain auto parts store brands...) usually have weak, inaccurate or just plain ****ty parts. ALSO! Before anything else, inspect certain parts physically.
- Did all units like TPS, IAC valve, etc. get replaced with quality parts? Oem is usually a good way to go unless runnin over stock hp.
- Load test battery
- Double check voltage at different point- alt., starter, etc.
- Drop gas tank (when low on gas) and check the pump/filter assembly and the tank itself. If this hasn't been done, there is a chance that there is crud in the gas tank. Just a thought.
- o2 sensors. Both of em. If not new, then probably bad.
- Pressure test at fuel rail.
- OP, you said the PCM was inspected. Was each connection tested individually? Cause that's a long process that may or may not give you results.
- Certain exhaust parts can clog and/or kinda fail. Exhaust inspection?
- Sea Foam (confirmed: Sea Foam IS made of unicorn buggers!) Sea foam can be poured directly into the TB. You need a buddy to keep rpm's up while you pour to keep it from stalling. Pour slow. You can also run a strong mix in the gas tank (assuming it checked out )

Ok. Like I said long winded. Hope something helps... Once again, just my .02...