A lot to update on this thread. Since my last post I installed the fenders and doors along with the engine and trans back in the car. Fuel tank, fuel pump, and oil tank went in as well.
I wired in the original bosch motronic system and attempted to start it a few times but had no luck. I had a friend of mine who's very familiar with the motronic system go through it and couldn't find the issue. Rather than start replacing sensors and patching up wiring I decided to start fresh with a MegaSquirt system. In retrospect I realized the problem with the bosch system was a faulty crank position sensor but I realized too late. This was something I had always wanted to do anyway and would've probably done in the near future anyway. I went with a Microsquirt based of a Megasquirt 2.
I was able to replace all the sensors with gm sensors that can be found just about anywhere for a fraction of the price. Being a diy system, I was able to get the standalone ecu wired and running for possibly less than the cost of fresh sensors for the old bosch unit. This includes new wiring. Unfortunately I didn't snap too many pictures of this process. I ended up putting the ecu under the seat in the factory position along with the new fuel pump and ecu relays. The wiring passed through the original hole by the rear seat and I created and engine harness wrapped in insultherm high heat wire loom.
To make wiring a little easier, I switched to s197 mustang high impedance 24 lb injectors as well. After finally creating a base tune based on what I could gather of the original ignition and fuel maps online, the car turned over (although a little rich)!
Motivated that I would soon be able to take the car for a drive, I finished a few loose ends I had in the suspension and installed the calipers after rebuilding and painting them. I finally bled the brakes, adjusted the clutch and throttle pedal. After a few more days of tuning I got it running well enough to do some street tuning. I put the bumpers, decklid, and hood on and went for the first drive in almost a year last week.
Still have some panel gaps to adjust and have to lower the rear a bit more. The interior is all wrapped up too. Suspension still needs some aligning adjusting and the tune still needs work. Overall I'm very happy with how it drives. The suspension is tight but not harsh at all and the cabin noise is minimal. This is how she stands now