Swapping your 3rd Gen 5.9 Cummins from and automatic to a manual transmission is not an easy process, but most who have done this swap would say the effort required was well worth it.
There are 2 main parts of an auto-manual swap:
1. The physical transmission, wiring and other hard parts that need to be installed
2. Re-programming your ECM from an automatic to a manual calibration
This article discusses some of the issues that may present on the electronic side of your swap:
Auto and Manual ECMs are the SAME hardware:
Lots of guys will scour the web looking for a “manual” ECM as part of their swap. This is unnecessary and may cause you more problems than you realize, especially if you are running a tuner already:
If you are running a tuner already, it is likely locked to your trucks VIN and the ECM serial number. While the new “manual” ECM you located can definitely have the vin re-programmed; the ECM serial embedded into the hardware cannot be re-programmed. This will result in your tuner/tunes no longer working on your truck after you swap the ECM without buying some sort of license from the Tuner Manufacturer.
The solution: Just have your ECM programmed with a manual calibration through a custom tuning provider such as 5-9 Diesel OR you can have the dealer do it (if you can find one who remembers how on these trucks).
Throttle Range and P2127 Code Issues:
On 03-04.5 model year trucks that came from the factory as an automatic trans truck, you will likely run into an issue after your swap where the throttle only reads up to 75% even though you have the pedal to the floor AND you most likely have a P2127 Code:
The short version of this story is, the auto trans trucks used a different APPS (TPS Sensor) than the Manual trucks did, and you need to address this as part of your swap or you will only see 75% max throttle after all of your hard work.
Fortunately, 5-9 Diesel has you covered:
This kit will provide the wiring harness and de-pinning tools needed to convert your 03-04.5 under battery APPS to the more modern 05+ on-pedal APPS; eliminating the 75% throttle issue and the common issues suffered with under battery apps failing do to corrosion.