If you have an 03/04 common rail that you have done a manual transmission swap and downloaded smarty software, you now have a 2127 code. Also the pedal is dead for some travel in the beginning and has only about 75% total throttle percentage when hooking up a scanner with live data.
The reason for this is the software they provide is for a later model 04 325hp Manual trans truck. This truck came factory with the under battery throttle position sensor which works differently. It has 2 voltage output circuits, instead of the earlier model sensor that just have 1 voltage output and an idle validation switch.
The proper way to fix the problem after the Manual Transmission software download is to install the UNDERBATTERY APPS SENSOR MOPAR PART# 53032456AE. You will need the throttle cable that goes with this sensor. You will also need the 03/04 DIRECT WIRE HARNESS that I make.The harness can be purchased on the 03-04 under battery APPS page.
There was a time in the past I offered a sensor that bolted to the existing APPS bracket on the side of the engine and you would run 1 extra wire down to #16 of the ECM plug. That sensor voltage curve only would achieve about 90% throttle. That created issues because most of the customers were building high horsepower trucks with stand alone transmission controllers or would have a fueling programmer that needed to see 100% throttle.
I have had customers use the alternative sensor after the swap that didn't notice any decreased power from the 10% lack of percentage, especially since the smarty fueling tunes greatly overcome that. If you have read this and want to go with the alternative sensor which makes the job a good bit cheaper and easier I could provide one upon request. Just send me an Email.
The main reason I offered that option is because years back the under battery sensors were on NATIONAL BACK ORDER for a very long time.