Converting an auto ECU for use with a 5-speed?

[Forsaken]

I have a buddy who I will be helping with a 5spd swap this coming weekend, and I was wondering if there is a way to convert the automatic ECU to work with a manual. I wasn't able to find anything on it with a quick search, but I have the auto ECU from my swap sitting on a shelf, so we have two to work with if I end up screwing one up... If infact it can be done. We're trying to avoid paying out the ass for one right at this moment, or having to wait until something good comes through the local scrap yard since its currently his daily, and the auto is on its last leg.

The one I have is from a '96, and he's converting a '97. I know there are differences between the two (I have the PDF for both), but having said that, I'm running the 5spd ECU from my rusty '97 in my current pathfinder. From a thread that I can no longer find on another forum I remember something about the main difference having something to do with throttle position tracking? I will be studying the PDF closely here before the weekend, so If I do find a way to do it before I get any replies I will be sure to post it.