This is just a guess and the info I have gathered. Anything from 96-00 manual and auto both use different ECU. But basically the same ENGINE harness. The only difference is that the auto ENGINE harness has extra wires for the auto transmissions. When doing a manual swap, if your truck is 96-00 and your parts are from 96-00. You can repin your auto harness to a manual ecu with the correct connectors. I believe that each year up to 00 uses different ecu connectors for manual and auto.
Anything from 01-02 is plug and play. It's simple as swap the manual and swap in a manual ecu of same year.
There are different types of ecu.
Example:
5VZFE M/T 4X4
5VZFE A/T 4X4
5VZFE M/T 4x2
5VZFE A/T 4x2
And again this is a guess, I think you could run into a problem if you use your ENGINE harness. Since you don't have 4x4 option neither does your ecu. This could mean that your harness might be missing few wires for that setting.
You could probably get a ENGINE harness and ecu of car parts. I did and I payed about $200 for manual Engine harness and manual ecu.
Otherwise you'll probably need to trick something or splice into something. [MENTION=22515]yotatech[/MENTION] there's dudes that have done many swaps of all kinds. I'd ask them
I'd also compare ecu wiring diagrams of your truck and donor.