Try this trick. Go to car-part.com (search engine of salvage yards). Key in make/model/year and such. If there are sub models, the web site will ask additional questions.
For the 1996 Model year, a search on the gas tank does not ask any additional questions. Conclusion: the gas tank is the same for the V6, SOHC, and DOHC.
When searching on the fuel pump, it asks for the sub model. Conclusion: there is a different fuel pump for the V6, SOHC, and DOHC.
I am not a Cobra expert. I suspect the difference is the higher flow Cobra pumps (just a guess on my part). In any case, there has to be a difference or the salvage yards wouldn't bother tracking it.
I think the 96-98 Gt and 96-98 Cobra tanks are the same. The 03-04 Cobras are different, they came with the dual pumps. So they have a different pick up, and they are baffled differently on the inside. And all 99 up tanks are return-less systems so there is no return line to the tank and no pressure regulator...
Both cars use return style systems. The pump in the Cobra is the single 170lph unit, the GT has a single 110lph pump (the 98 got the cobra pump). Fuel lines are the same. The fuel rail on the GT actually flows more than the stock cobra rails and can support a little over 500rwhp. The GT sports 19# injectors while the cobra has 24# units, both are EV1 style. Both systems are set to operate at 39.15 psid.