He did the fuel pump and filter...so I was thinking about fuel delivery from left to right lobe...the sending unit fails too. But, unless it can fail 'soft' or unless OP never fills up his tank, that wouldn't explain his symptoms if they've been persistent for a while...and it sounds like they have been.
OP...as mentioned, scan for codes. The car will have something recorded about what you've been experiencing.
Oh, and the other thing is that if any of this work you did was prior to these symptoms, and you got them shortly thereafter, consider an issue with aftermarket parts, especially electronic things. You didn't happen to do something else prior that you don't think is in any way related, and thus didn't mention it, did you?
I'm so depressed. No one wants to come see me in NYC: Sat, Oct. 8, 6 p.m. at Greenwich Village Comedy Club.
Mangofy your E46!