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Seems like you may have a VIN mismatch w/ the engine (or Flagship 1 is mistaken/wrong). That happens when engines are swapped out, You may need to get the engine serial number, but it is difficult at best! The engine serial number is located on the left rear corner of the crankcase.
Clearly you do not have an '03 engine, but FS1 says the VIN indicates that you do - that is why I am suggesting the engine was swapped and I do not know why you could just tell FS1 that and let them help you. Also, as I posted above - one of the ones you bought from FS1 clearly was labeled for manual transmissions.
No FS1 is saying the computer that was in the truck was for a 03 and not an 05 the computer I bought from them that they said matches my vin won’t work . I Am trying to find a computer for the 05 so I can get my truck back running
If they say that your VIN is for a manual, but you don't have a manual, then I don't blame them for not wanting to tell you what you need.
Also, we don't REALLY know if you have a late '04, or an '05, 06, or '07. So maybe they just are trying to avoid sending you something that they think might come back.
Maybe Razzi will tell you specifically what to order, but it seems you are just going to have to take your best shot based on what you know about your truck.