I ended up taking my car to a trustworthy independent shop. They had the car for 3 days and could not find any smoking gun (like the original shop and even BMW dealer had implicated previously). They checked out all things related to the OBDII codes and found nothing wrong with any of them. I told them about the DME problem prior to their inspection. They gave the car back and, by process of elimination, agreed that it was probably the DME software, as referenced in OP.
Next, I go to the BMW dealership (as the independent shop was not capable of "reprogramming" DME, and they told me they didn't know of any other indies that were, only BMW dealerships). I tell the BMW service rep everything -- that i've pretty much done the leg work, just fix my DME. He gives me the standard brush off and says they'll "throw it on the computers and they'll tell us what's wrong." I was entirely incredulous that they and their computers would come to the same conclusion that I had -- and would anyone be surprised to hear that they didn't?
I go back to pick up my car and he says "Yup, just the MAF. We replaced it. You're good to go." (I paid $50 deductible on the CPO warranty). He also said the readouts showed the car running lean, which is the cause of the lack of power. I knew it wasn't the MAF but also knew I couldn't convince him because he a) wasn't a mechanic b) he didn't listen to a word I said before.
I drive the car off the lot and up the first hill upon leaving the dealership and, of course, the problem is still there. I made three more right-hand turns and pulled back into the service center, walked up to the rep, told him the problem is still there and asked for the head mechanic. He retrieved the mechanic, I told him of the issue; he knew of the DME software glitch, unlike my rep, and willingly went for a ride with me, so I could demonstrate the issue. Same hill, same hiccup at 2500-3000, I'm not crazy, mechanic is totally sympathetic.
End result: BMW dealer keeps car for about 3 business days, pulls DME ships it to New Jersey for reprogramming (so i am told), has it returned, plugs it in...no more problem. I was one month from my CPO warranty expiring, otherwise I think I was looking at a hefty bill (~$1500 to replace DME, not sure what "reprogramming" would cost -- too much, anyway)
I also wanted to ask again to any posters: have any of you experienced the problem AFTER replacing stock paper filter with a "high flow" filter, like K&N?
Sorry for the saga, but that's exactly what diagnosing this problem turned into for me. Best of luck to the rest of you.