Thanks for the information. I really appreciate it!!
I was not provided the correct motor mounts as they were the big block mounts and the obviously I have a small block. So, I had to fabricate some motor mounts that put the engine just about in the center of the cradle. The trans tail shaft is dead center to the frame members. Yes, I could use the factory shifter and not have much of a problem, but I want to use the short shifter, hence the shifter plate protrudes more to the left to the very edge of the fiberglass and also above the fiberglass tunnel as well. All of this should be able to be covered by the interior shop. (I visited him yesterday)
About my pipes, let's not discuss that yet. I have a set that is wrong for the car and will need to be "reworked", along with the side pipes. These are generic standard side pipes for a shorter cobra as I do NOT have any of the factory exhaust that came with this kit. Hence, I am fabricating everything to fit.
I have a friend here in NC that has an Excalibur that is basically a CR in almost all aspects of the car. Just a few differences. His tunnel and t5 is also slightly to the left, but he has the stock shifter. He also has a custom made interior that is so thick and padded that it masks or covers any problems on or around the tunnel. So, my assumption is that the shop that will do my interior can do the same thing.
I also talked to another CR owner that built his in the recent past and he had the same problem. He just "shimmed" the left side of the tunnel to come out just a little bit to allow for the installation of the boot and shifter. I will most likely do the same before taking to the interior shop so it is all solid for him to work on.