The missing part to remove the blower/heater and internal wiring harness was to disconnect the remaining lines that travel through the engine firewall. In hindsight it is obvious, but when you are sitting inside the car trying to figure out why the heater core doesn't want to come out, it can be frustrating. Unfortunately Domino has spewed oil all over the place inside the engine bay, so it made for a messy time.
And the rest of the wiring harness came out without too much drama.
This is the harness fully removed from the 2001 RS.
Here is a wiring harness from a 2005 STI. These two will have to be merged.
Here is my version 8 JDM STI ECU and the free AVCS wiring JDM Racing Motors provided with my order.