Another option is to buy one of the Ford Racing "Aluminator" short blocks like the one below:
http://www.roushyatesparts.com/4_6L_...6009-a46sc.htm
For $4300 you get a brand new aluminum short block that you can bolt your heads, supercharger, and all other accessories on. This will shed about 80 lbs off the Terminator engine that has a cast iron block....which weighs around 800 lbs as a complete engine, which I believe is heavier than a FE cast iron engine. I'm sure most people would agree that taking 80 lbs off the front of a Cobra can be valuable.
I highly doubt a local shop can rebuild your engine for less than $2500 if it needs a crank and other parts associated with
oil starvation. These engines didn't like being run lean and had a tendency to severely scuff pistons and damage bearings in the process.
As part of the development team for the 2003 Terminator program with Ford I can attest to this first hand, seeing this on many test and customer cars.