Truck still giving me headaches checked out the fuel pump its pumping fuel at the right volume so it is ruled out. The timing of the fuel system seems to be out of wack as you pour the fuel to it, the truck seems to have a secondary humming noise. Truck is now starting to balk quite a bit in other words it hesitates some times when I pour the fuel to it and when it does it puffs dark smoke any ideas? Truck is a 01 2500 ram diesel 5 speed put a motor from an 02 in out of an automatic

 

Did you replace all the ECM/PCM boxes to match the manual transmission? The programming for auto versus manual is different, and they rely on different signals to make changes in the fuel delivery.

 

Motor came complete the only thing we had to do was add the alternator change out the fly wheel and hook up the electronic connections. I got it checked over at the dodge dealership got a clean bill of health it ran fine for a while then started to act up.

 

Checked the codes on the truck it throwing p1693 I checked all threads on this site that relate to this and none of them have identified what the code is does anyone know?

 

Its a companion code. You need a code reader to get the codes out.

 

The electronics are not compatible. The auto trucks take into account signals from the transmission and adjust engine parameters based upon that input. A manual truck doesn't give those signals, and the ECM/PCM won't be able to figure out what it should do. I'd see if you could borrow an ECM from a friend with a manual truck (or use your old one) and see if it makes a difference.

 

If you do not know what is wrong " NEVER " swap computers , these computers almost never go bad by themselves , a bad computer is about 99.99% made bad by something on the outside killing it , so if a solenoid or short some where else on the truck damaged the computer , then when you put another computer in there as a test/fuse , and blow it up , now you need to by 2 new computers .
Next just a lack of info makes it harder to help , as an example , you said you check the fuel pumps volume , which pump , and I would suspect you did not check the volume [ a rare tool , checking volume ] , pressure is what is usually check in diesel fuel injection , and coming from lift pump .
Did you check with a good parts house for any variation in the computer compatibility ?