So we rolled our 99 Durango mud truck and found a 97 Dakota shell...... It was a 5.2 manual transmission truck we took the 5.9 drivetrain outa the 99 Durango and put it in the Dakota used the 99 harness and computer. We get power and fuel to everything but it won't turn over ... We have not replaced the steering column yet for the right shifter but we are in park. Does it have something to do with the column or a neutral saftey switch issue?
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When you switched the 99 harness into the 97 shell, what did you do under the dash? The neutral safety interlock goes through the clutch pedal.

For a manual truck, the clutch pedal plugs into a green connector in the interior firewall, and the harness is grounded by the transmission.

For an auto truck, a jumper is placed in the clutch pedal connector, and the wire is grounded through the NSS on the side of the transmission.

The shifter is irrelevant on 97-03 dakdur, since the circuit is decided by either the M/T clutch or the A/T NSS, and not by a linkage on the column or floor shifter. Mine is an auto, I tapped that jumper and grounded it through my race shifter's NSS and left the factory transmission connector unplugged. PCM is perfectly happy with that (along with a few supporting changes in programming to get rid of CEL's by making it think it is M/T)

 

We just changed the engine harness that plugs into the computer and the fuse box

 

You'll need to address the interior harness then. Did the harness swap include the transmission harness? That should all be on the engine side of Connector 200 in the driver wheelwell. The cabin side of Connector 200 will need that clutch connector jumpered out.

 

Here is what you are looking for. Your best bet will be to get the jumper from a junkyard, or cut and splice the wires. I tapped the loop and ran it to my shifter, which then grounds it in neutral.

 

What flywheel did you use?