4L60e to 700r4 swap

[1962 Panel]

Quick question for anyone who is familiar with how a 4L60e communicates with the motor in a 1993 c1500. I drove a 1993 c1500 with a 350 for a while that needed a transmission when I got it. I knew it had a 4L60e in it but I was unable to find a reasonably priced unit so I put a 700r4 in it that I got for a steal. The truck would sometimes idle rough and stall when put into gear but I always assumed it was a bad intake gasket because it did the same thing before the trans swap. Eventually I ended up selling the truck to a friend of mine and he replaced the gasket, and confirmed that it was leaking. Long story short after redoing the intake it runs even rougher apparently and stalls every time it is put into gear unless you two foot it to keep it going. My buddy insists that it is running like crap because the trans isn't communicating with the ecm. I don't think this can be possible because the truck idles rough even when its in park or neutral. I also don't see how lack of signal from the trans could cause it to stall when put into gear.

Can anyone weigh in on this issue because I'm trying to help him figure this out because I am the one who sold him the truck. Thanks in advance