That is one of the possibilities.
Do you have any local driveshaft shops? I have a 98 Cobra just like you, and I had an aluminum driveshaft custom cut and balanced for $199, and it was hard to beat. The aftermarket driveshafts are nice as well, but I liked the idea of stimulating the local economy and that it was perfect for what I needed.
Viper T56 is an industry term that is somewhat misleading, chances are, it is not coming out of a Viper, but it is built to the same internal specifications of the Viper T56. There are actually quite a bunch of cars running Tremec T56s, but the Viper is bulit to the most powerful specs (some Aston Martins, Camaros, Cobras, Vettes, and Vipers).
Did you get a 03-04 Cobra bellhousing with your transmission? I could be wrong, but I believe that'll just bolt right up since the 4.6 block was the same throughout the 96-04 Cobra run. However, I don't believe your 98 T-45 will.