I'm sure most of these questions have already been asked at some point, but:

I recently acquired a 2001 5.9 Magnum as a possible engine replacement for the 5.2 in my 99 Dakota 4x4

Just under 40,000 original miles, I couldn't pass it up.

Of course, the engine wiring harness is destroyed.
Will my '99 5.2 engine harness work as a replacement for the '01 harness?
Id love to look for obvious differences but I don't have much to work with, kind of a hack job engine pull.

Will my 1999 5.2 ECM work with the 2001 engine?

Both engines had automagic transmissions.

Is there anything else that needs to be considered for this engine swap?

My hughes cam, freshly repaired intake/plenum, and a myriad of replaced parts would go in with the 5.9 (in theory).
The truck is a dedicated 4x4 I use for light offroading, camping, hunting ect. The 5.2 in the truck is tired, not near dead, but tired. I plan on keeping the truck. I already had the trans rebuilt, now I'm in too deep.

Thanks for any input.

 

Should be able to drop it in, hook it up, and it should run. Wiring harness is the same between 5.2 and 5.9, and I don't think any sensors changed over those years either. Only real difference is the 5.9 is externally balanced, and the 5.2 is internal. So, gotta use the original 5.9 balancer, and the correct flexplate for the 5.9.

Given the changes you have made to the motor, gonna need the proper tune in the PCM for it to run right though.

 

Injector connectors will be different - EV1 and EV6. Other than that, PnP.

 

I noticed the different injectors, my 99 intake and everything on it would go on the 5.9.

I've ran into an issue with the externally balanced engine, I found a crack and bent bolt hole in the flexplate. Can I not put any 5.9 flexplate on this engine? I'm assuming its balanced to that specific rotating assembly.

What are my options? Take it to an engine place?
Buy a balanced rotating assembly?
I was trying to avoid taking the heads off, they are aftermarket heads and in theory are still very fresh yet. I know they easily crack so I am avoiding taking them on and off.

 

Very common thing. You can get a 5.9 flexplate off Rockauto I believe. They are all weighted the same to my knowledge (mass produced).

I might even have one off my junkyard engine, since my 408 is IB and uses a 5.2 flexplate.