Help with stock EFI

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?
I can’t really answer your question sorry. But at the very least the Speedo won’t work and there may be some weird shifting problems with no speed signal. And it will throw codes and possibly trigger limp mode. Those are just my thoughts on possible problems. None of that is definitive.