Pi swap questions

I've got a early 99 gt with a non pi 4.6 and a t45.
Also, I'm gutting a 01 gt with a pi 4.6 and a tr3650.

Question: is this a simple drop in and go? Plug and play situation? I'm taking the harness from the firewall and everything attached to the motor and tranny, is the 99 non pi computer going to work...what else am I going to run into?

Thanks in advance
 
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