I don't know. In 99 they had a Tremec built T45. I haven't heard that they have changed, but it would be nice if they did.
But as far as the 13.8; SVT is conservative in their performance estimations. My manual says that my car, stock, runs 0-60 in 5.9, and the 1/4 in 13.99@100. The best completely bone stock, down to the filter and tires, (Completely stock) I've ever heard of, with a time slip, and many credible witnesses including Bob Crosby of the Corral, is a 13.08. So with descent driving, and as long as you don't live in Denver, I think the SVT numbers are a lower bound.
Have you heard anything about the axles? From the Cobra R, harder axles do a IRS good.