Stuttering under acceleration *need help quick*

I have a 04 LB7 that is having a problem with stuttering. It happens when i get on the throttle and reach something above 2300 rpm. I first thought it was fuel pressure so I replaced a Fuel pressure regulator (it was putting out a code) This did not fix the problem. I then logged balance rates and found 4 bad injectors. Took it to dealership and they replaced them for me and I still have the problem. I have a P0101 MAF code and a P0089 code for the Regulator. The regulator is because I have a K&N FIPK intake and apparently it doesn't work well with the MAF sensor. I would put the stock intake back on except for the fact that I bought the truck with it and the dealer didn't give me the stock filter housing. What I have noticed today is that right after a full reflash the problem will go away and stay gone aslong as I don't shut the truck off. If i shut the truck down and then restart it my problem comes back and stays there unless i do another reflash. How can I go about troublshooting this? I have to tow a trailer on the 9th and would love to have this resolved before then.

Here is a link of more detail on diesel place
http://www.dieselplace.com/forum/sho...d.php?t=312209

I Have included a log file that shows the problem at Frame 153

A dirty MAF can cause the PCM to dump fuel,
possibly your MAF needs to be cleaned or replaced.
Is flashscan set to clear DTC's after a reflash?
This might explain why all is well after a reflash.

the story on the MAF is this:
I have cleaned the MAF with MAF cleaner several times even before this is happening.
My MAF in a log is reading more air flow than what is expected in the tunning file. (about 1lb per min more than tolerance) I have a K&N intake. I have researched this intake and found that the MAF is moved closer to the filter for one reason or another. This placement is in more turbulent air and causes the MAF to get funny readings. I am going to try to load my stock tune in and then create a map of what the MAF is reading on a stock tune. I will compare this to the expected air flow and take an average percentage difference. I plan to apply this change to the MAF scaling table in attempt to "tune" the MAF to the intake. I will also apply these changes to my modified tunes and see if the P0101 code is cleared. With any luck it will also get rid of my stuttering. Am I on the correct path??? Anyone ever done this?