So, after a long battle and roughly three trips to the dealer, I'm thinking this is finally fixed.
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First trip to the dealer ended in them just repeating what I had already done, replacing the MAFs. Now, I had already informed this of this thread and issue as well as the fact that Nissan was aware of the issue, but I'm not sure where that information went because they preferred to just repeat steps. I wasn't too upset with this since, under warranty both stock MAFs were only $100. Honestly, if I would have know that I would have done that to begin with and saved my time and a few bucks. The down side is, I'm 99% sure that the aftermarket ones I put in are fine even though they told me "they're just not working right." I pretty much told them that I would be back very soon.
Light came back on and I was back in the shop again with a big "I told you so" grin on my face. Again I reiterated what was believe to be the issue and that they should probably start there or at the very least call Nissan and again I'm not sure where this information died... This time, they called me to tell me it was finished and that there was a known problem with a bit on the ECM. They said that they flashed the ECM with an update and did all the relearn processes and that the car was ready to be picked up. Before I even got off the phone I told them "that's not it and I will probably be back." To which they told me "well, everyone else who has had this issue and had this done hasn't been back, so it's probably the problem." I proceeded to tell them why, if I understood what the software change was actually for (as he sort of broke it down for me originally), I would be back in shortly. Since the change didn't address a root cause but rather how the ECM reacted to a code being thrown in the first place. (Honestly not sure why this was even a question but maybe I just have the upper hand as RCA is kind of my profession...) They also said that they would like if I didn't plug in my ODBII reader until my next oil change as they were concerned that it may be interfering. I'm not even going to go into the detail of how I picked this apart on the phone. Again, I basically guaranteed them I would be back. So I picked up my car...
...and she threw another code the next morning. I was too busy with work and other commitments to bring it in right away - even through I wanted to oh so bad - but got it in the following Friday. Again, I repeated what I knew and what I believe to be the issue. Pretty sure it didn't get much further than it had before but this time they at least called Nissan. "Soooo, we called Nissan and they said that it's the throttle bodies." To which I responded "and what was it that I was saying all along again?..." So, apparently they don't have a procedure for just cleaning and replacing - though I come to find out that they tech did clean them because he said they were destroyed - so they had to order two replacements which after a short debacle with the shipping truck arrived and were installed. I picked up my car this time telling them "I'm fairly certain that I won't be back until my next oil change now, you know, seeing as how you finally did what I was suggesting all along."
So, I have had my car for a few days now with no issues. I'm not going to count my chickens just yet but as I said, I feel pretty confident.
I understand the process that they had to go through - as I have had to work in technical support myself and sometimes you just have to redo things the customer has told you they've already done - so I'm not upset about that. That being said, it would have been nice for them to at the very least take my advice, look at this thread, and call Nissan to confirm a known issue from the start.
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At this point, she's basically back to normal, for a car with 50k+ on it. The throttle response is a little off but I think it may still be relearning. Also I'm attributing this to stock air filters and oil that could probably use getting changed due to driving on the CEL and limp which, if I understand correctly, makes the car run rich.
I do kind of miss how loud my exhaust was during this whole ordeal but it is nice to have power back.
Thanks again to everyone involved in this thread, the advice, and the information. (Even though I couldn't get it into the right hands in the first place...)