97 motor swap

[l79m20]

I have a plain jane 97 truck with a 4.3...Motor is bad so I found a new one from a 2000. As far as I can tell the only difference is in the computer. My truck is a 5 speed and the 2000 came with an auto. I talked to a mchanic at the dealer and he thought it would be fine to use the 97 computer as it would be trying to recognize a 5 speed and the 2000's would want an auto. This truck is just a work truck that we use and abuse. Any suggestions or potential solutions for problems would be appreciated!

Thanks