IIRC, the '03 still used a Powertrain Control Module (PCM) to control the 48RE transmission. The PCM is behind the passenger side battery. The ECM will probably be the same for both the manual shift and automatic, but as posted by HBarlow, you need to check the part numbers to make sure.
Bill
I don't KNOW but I'd guess the answer is NO! I very seriously doubt the ECM is interchangeable between an automatic and manual truck because I think the ECM plays a role in controlling the 48RE, right?
I think you'll have to find an ECM for a manual six speed truck.
You can double check my opinion by comparing part numbers.
When you learn the correct answert to your question please post it here. I'd like to know the answer.
I guess the you did not understand they both have the same p/n the one i found in a NJ junk yard from a automatic truck has the same p/n and mine
I want to hear more about the rod going through the side of the engine if possible.