Help with stock EFI

Lots of people have used the 5.2 and are happy with it in an A body. They run pretty hard and are great little engines. Do a search here.
Basically what I am advising is find a complete 2wd truck, regardless of if it’s obd1 or obd2 and use everything from it. It will make the swap simple require very little to make it run in an a body. When swapping transmissions, flashing ecu’s, de pinning and changing sensors all between obd1 and 2 it will require time and lots of reading in factory service manuals to get it all correct. You’re on a timeline so my advice is to push the easy button.
I’m sure that would have been the easiest, but he really wants the 360. I’ve already got the engine pulled and cleaned up ready to paint once the oil pan arrives. I’ve got the harness and ecu from the donor truck. I’ll go back and get the pcm and the rest of the harness to the one plug. The 46rh is in good shape and free so budget wise I want to give it a shot.
The question I have is, what if I use the 99 ecu with the 46rh without reflashing it or anything? Does the ecu have to detect the transmission for the engine to run, or will it run fine but just have error codes that I will never know about unless I hook up a scanner to the obd?