I have found an 88 350 TPI engine with the computer but no transmission. The original trans was an automatic, can this computer and PROM be used with an 87 700r4 that I have? Will I just have to add the wiring for the lockup function or does the PROM have to be programmed to lock up the converter?

You've confused me as to what you're trying to put into what.

In general, between auto and manual apps, the computers are the same, but the calibrations are different.

You do NOT want to try to run a 700R4 using a manual trans chip.

How about the other way around
Automatic chip with a manual?

At least it won't hurt the transmission that way.

Driveability may not be perfect, but people have occasionally done it that way and made it work in some cases. OTOH, I wouldn't say that's really the right way to go about things IMHO.

As to why this is, the throttle follower routines are different between auto and manual apps. Also, the code that controls TCC lockup in an auto isn't present in a manual bin, since it's normally replaced by the shift light code.