Not sure how I missed this thread. Hopefully this thing gets built, looks amazing! I love my Cobra too much to transplant the drivetrain but it would be a blast to drive!
BTW...the 99 long block will not support the boost from that Eaton. O John Coletti blew up several motors throwing rods through the block when he tested the Eaton on non-forged internals. He finally convinced Ford to beef up the internals. He went from $7 rods to $57 rods. Talked about in this book which is a great read:
http://www.amazon.com/Iron-Fist-Lead-Foot-Terminator/dp/0595409709
Let me know what you're looking for in the way of parts. I have a spare Eaton I might get rid of but you would still need the upper intake, intercooler, heat exchanger, etc. I know lots of Cobra guys so I can probably track stuff down rather quickly for you. Actually a buddy of mine is going turbo this week on his but he removed his Kenne Bell for this: