Hi SR:
I thought I'd throw my two cents in. Here are the passenger and driver's side shots of my headers lined-up with the sidepipes.
That is my car, CSX4786.
I have been to the HST plant regularly to inspect the Cobras for Gary Davis at Shelby. Of course, the VIN tag, MSO and final inspection are performed at Las Vegas. I started back around 4778 and am still doing it. So, I have seen your car close-up many times--that would have been around September 2005.
I am sorry for all the trouble you have had. But, as you said, there are some real good people working at Shelby.
I started measuring the orientation of the foot boxes right around this time period after Gary told me to take a closer look. I think he said on the previous car he had noticed this. It is not something you would necessarily notice when the engine is missing. There is a fixture at the plant to place the box; if I remember, there was a personnel change and instead of orienting the foot box without the throttle bracket and bolt, the bracket and bolt were in place.
As for the trans mount, right before my car , it was changed to accept the Tremec by default. I know on my car I was concerned I get the 5-speed mount, since that is what I am using.
So, I hope your story has a happy ending and wish you the best getting your car on the road.
BTW, I have a bunch of photos of your car, as it was being built; I'd be happy to send them to you.