I know 03 doesn't, the motor in my 04 is from an 03 (root of the problem)

I have a bullydog already on my truck and currently am happy with it (guess tuners are like opinions), so spending another 300-500 for another one is not really first choice, hence why i am looking for other options

 

Well since your truck now holds an 03 motor there is no real way around the problem unless you re-tune to a custom to delete the DTC or try swapping computers to an 03. I cant tell you that switching to 03 computer will help but since you already have a programmer i guess id spend my money on a PCM.
If it was me id sell the Bullydog for a Custom tune, its a win, win you get a way bette tune then the Bullydog will ever give you and you solve your problem.