You could always try a very short run with no Air Filter if you wanted to test.
I use the Holley Power Shot 'oiled' Air Filter with the SLP Lid. I like that fit. Personally, I just stick a new one in their every other oil change. Call it overkill, but I don't trust my technique in re-oiling. I clean the MAF every 2-3 months.
Brad..Upon close examination of your Tune & Log, it looks like even though your LTFTBENS average +/- '0', the delta between Max and Min indicates you are positive most of the time. So, here it was I did. In the attached Test Tune (yours altered), I added +7.5% to the entire MAF Table (B5001). That should not only keep you in negative Fuel Trims, but should also solve your Commanded vs Actual AFR in PE Mode. You might average ~ -3 to -5 % LTFT's, but really thats O.K.
I also adjusted your VE Table (rough hand-smooth). You may find after running the new MAF Table, that your VE Table will come more into line.
Thats my best take on it. Keep checking for any intake/exhaust leak..especially near the MAF. But, you can always give the Test..a Test..
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