Compression Ignition Addict
Join Date: Feb 2010
Location: Fayettnam, NC (Centennial, CO)
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Same engine, I don't see why not. Not sure if the 5 spd and 6 spd used different flywheels, but if I were a manufacturer I'd use the same flywheel between the two for cost efficiency. I'm sure you'll need a new clutch assembly to go with it, so invest in a quality kit that suits your needs.
The only things I see that could be an issue are the crossmember position/bolt pattern, the trans to t-case mounting surfaces, and the length of the driveshaft(s). Best to look up specs on all of those before you commit to this.
Also, you may want to check the length and diameter of the trans input shaft.
If all the dimensions and mounting surfaces are the same, there's no reason why not.
But how do you know the trans is even good? What a junkyard says might not always be the full truth, and they probably wouldn't even know for sure in the first place. Without seeing it run...
EDIT: Wait... reprogramming? Are you swapping from an automatic or do you have a 5 speed? If you're swapping from an automatic, that changes things a little.