Ok after looking at the file this is what im concluding: Please verify...
-you indeed have the 04 trans and gearing has been changed
-your running the 03 NA file
-all the security has been removed from the pcm.

if it is still the original PCM harness and BCM, i don't see why your key or security would cause this issue. further more, if it were security i would think it wouldn't start at all. that being said, you could set the security all back to normal and i don't think it would change anything. when i swapped from my DOHC to the 98 L36 and trans i did not change any of the security tables and it all runs fine. now im running with my topswap and it still is great. so i don't these files needed changing.

It has been a known issue with the 2003 trans only working with 03 pcm. it is possible that the 03 bin file you are using is not compatible with the 04 trans. I can send you 2002 l36,l67 bins and 04 NA,SC files as well. your pcm will not accept the 04 but they might be a good ref for you. your pcm should accept the 02 files if not you may need to swap pcm's

if that doesnt work, i would contact overkill as you get much more for your money vs zzp or intense.

 

I was talking to intense they say they can do it for 175

 

Would an aftermarket alarm come into play with an of this? It shouldn't right?

I'm just starting to think when I order the SS kit I had planned on sending the PCM in to be flashed, to avoid the security relearn. However, I've heard of issues about getting incorrect bin files from certain places... Should I have them send me the file, have someone look it over and load for me?

Sorry for the hijack, I just don't want to end up with a PCM that won't work (have an 03).