My opinion,
Since the original engine is gone, and the car is already repainted in the wrong color, I'd build it like you want to and save the original rear center section and tag ( It's the only "E" unique piece left). Restoring the car to concours condition would be expensive, and hunting down all the missing parts would be time consuming to say the least. What you'd end up with is a car that would appeal to a VERY small segment of the mustang community, and if you had to sell it, you'd be hard pressed to get 1/2 of what you had in it, even if you did a lot of the work yourself. A six cylinder car missing it's original engine, even one of 96, wouldn't be the car to restore to concours level unless there was some sentimental attachment to it. 69 fastbacks are so popular because of their styling and their "muscle car" image, and you'd end up with one of the slowest 69 fastbacks ford ever manufactured. ( a 6 cylinder, coupled with a 2.33 gear and a tight converter ) From reading your posts, it sounds like you really want a performance car and that's not what you'd end up with when your done.
Before all the six cylinder fans on the forum crucify me, I am a straight six fan, my first car was a 66 convertible with a 200 six and a 3 speed stick, and I still miss that car (Don't miss that trans though
) I do know how difficult it is to sell a six cylinder car that's above just a driver level is though. A while back a friend inherited his grandmothers 67 6 cyl coupe. It was a 27,000 mile, mostly garage kept, original owner car, green/green, original very faded paint car. After trying to sell it for six or seven months for 8 or 9K, he finally took 6500.00 for the car, and the new owner used it's doors, fenders, and a bunch of small parts for a Shelby resto, then replaced the parts with Chinese stuff and gave it to his daughter to drive to school.
If you really want a performance fastback to drive and show, I think Kerry has the right idea, save up some cash, then sell your car as it is, and buy a 70 Mach 1 driver and restore it as funds permit. There are a lot of H and M code cars out there reasonably priced, parts are around, and you won't loose your A** when you go to sell it. ( remember, body and paint work cost the same weather it's a 6 cylinder fastback or a R code Mach1 )
Something tells me I'm going to get an earful now .....
John