A lot of time has passed since the original post, and lots of advice on which engine to get but I would concur with a stroked Windsor is probably right. SPF/Hillbank will try to sway you to Roush. My experience with Roush fuel injected was less than good, and recent tales of high
oil consumption scare me A friend has the carb'd version of the same engine in his SPF GT40 (done by Olthoff - good place to go) and he loves it. That said, there are lots of sources for stroked Windsors, so shop around.
Then you have to decide on the displacement. I always thought the 550HP Roush was a little much for the light weight of the Cobra (and several unplanned compression braking events more than confirmed that in my own mind). Someone mentioned a 392. Might be a little more manageable for street use.
Also recall that these are light cars in the rear with lots of torque and HP and that keeping the tires hooked up can be difficult, especially with colt tires on cold pavement. Both of my compression braking events were simply downshifting to make a left turn. My car had some kind of Goodyear Eagles. Supposedly good track tires after they warm up but not good until they do. I've heard Avons are good but consider getting some old style Goodyear Billboards!!!
On the SPF royalty. I don't think it's a huge amount, and I believe it goes to the Children's Foundation anyway. With the comparatively small number of vehicles produced annually, noone's getting rich from it.