Help with stock EFI

TT5.9mag said

On another note, if you do not use the 46re, you will have to get a manual trans ecu or have your current ecu flashed to remove all of the trans programming stuff. Both of which are possible but I had a hard time finding a manual trans ecu when I looked for one.

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My nephew has a private dodge truck bone yard and he has a truck that is the same year that had a manual transmission that i plan to grab the computer from. He also has the complete 93 dodge truck that I’m getting the transmission from. Would I be better off taking the computer from the 93? Am I still fine using the wiring harness from the automatic truck?