5.3 Engine Replacement - Wiring harness question

I have a 73 Toyota Landcruiser and I'm in the process of converting the current engine (SBC 350) to a 5.3L Vortec.

My question is in regards to the wiring harness;
The 5.3 was removed from a 2002 Pickup (running good) and the guy who pulled the engine did a great job at removing everything fully intact.  He left the entire wiring harness connected to every part of the engine, ECM, and Under-Hood Fuse Panel.  The only wires he cut was the wire loom going to the rear of the truck (lights, etc...) and the large wire loom going into the cab of the truck through the firewall (this is my concern).

The Landcruiser currently has a SM465 4-speed trans that I will bolt up to my 5.3 (bots right up by the way) - At this point I'm not worried about the emmissions sensor, the check engine light (will do later), etc.. I only want it to start and run.

Here are my questions for anyone that may know - any info is appreciated:

1.) Has the wiring harness been ruined by cutting the wires going from the under-hood fuse panel through the firewall into the cab of the truck ?

2.) What is required to simply get the engine running (without check engine light, emmissions, transmission, etc...) ?

My guess is that I will need to send off the ECM to be reprogrammed to bypass the anti-theft mechanism and that's about it - right or wrong ?

3.) Where can I send the unit to be flashed and what is the est. price ?

4.) Can my harness be salvaged ? Everything from the firewall forward is 100% complete.

Thanks for any info
Mike