You want the most flow and efficiency in the boost range you want to run. If you slap on heads that flow alot, that 17psi would be equal to 25psi with stock heads, but it's 17psi nonetheless, which will allow pump gas, cooler air, more timing, etc. What kind of hp would you like to make, and what kind of ET's? If mid 11's are ok with you, a good intercooler, cam and head work, and a TE44 is fun. I have serious traction problems with mine, but it does seem to run out of air on the top end. But an 03 cobra with the swaybar pulled, a pulley, K&N and sticky tires can run 11.60's. Hell, Bob Cosby was running that with a 99 cobra without a power adder, with some lightening, suspension work, and factory stock legal bolt ons. Stock long block. Ive seen it. If you want to put a spankin on them, you'll need to bring something bigger to the table. I know the cobras only have 50 more cubes than us, ( us...funny coming from a former 99 cobra owner) but they have heads that flow alot and they can churn out some serious rpms. TE-45's can make 10 second power, and add a good quick spool boost controller, ported heads, sticky tires and you'll have a hard time holding on. All the power is in the heads and the turbo. The cam would come next. The cam is the biggest factor with passing smog as well. If you want lots of power and you want to pass smog, keep the stock cam, or go no higher than a 206 cam, get the TE-45 or an equivalent, a quick spool boost controller, heads that flow as much as you can get out of them, and some sticky tires. Then start saving up for your next engine and tranny.
If you dont want to keep breaking parts, just get the TE-44 and the boost controller. I made my own, and it makes such a tremendous difference in the fun factor, its unreal. INSTANT full boost.