Just curious, can you cut out all the connections that you do not use anymore, such as the wiring going to the fuel injectors and smog equiptment? If so, what would be the proper way to do this? I wanted to leave the majority of the harness there and just cut off excess because I wasnt sure what could go and what could stay.

 

Not sure what you have done and if you'd want to retain any function of the ECM at all, like TCC lockup. But you have probably removed/ disabled the ECM and the CEL, and if so of course you could just cut the unused wires, there shouldn't be any power there anymore.
If it were me, I don't like to hack up original wiring, so unless removing the entire ECM harness I'd just fold back the unused connectors and tape them to the harness. Factory does this.