What are your goals?
Okay, Ive got a 97 cobra BUT its got a gt's 4.6l sohc 2V in place of the missing dohc 4V (not sure which year the motor is). Now Im new to the newer mustangs, so I dont know that much about them yet. But anyway, what Im wondering is would you save up enough $$$ to pick up a dohc 4V to transplant back in there. OR would you take the money and build the sohc 2V? I should be able to scrap together $1500 quickly towards a build, but to purhase a dohc, I can save for a while, no big deal. Further more, for the previous owner to put the gt motor in it, do you think he had changed anything in the electronics to make it work properly, or would it have been a basic "drop-in"? Or is there a different route you would take?
Since you asked for an opinion, here is mine.
Since $$ is a problem,
DRIVE IT just like it is. No one will know unless you tell them. If you have to tell your buddies something, say the motor is hurt and you are saving for a new motor.
Since you have a
real Cobra as verifed by the VIN, the car is worth something once the correct motor is installed. To sell it now is "buying high, sell low".
IMO, anyone that would put a 2V NPI-SOHC into a real Cobra is looking to make a quick $$. Therefore, it is reasonable they would have done the absolute minimum to do the swap. That means it is likely that most of the Cobra specific parts are still there.
Now onto your goals. Do you want to do the work yourself? How important is the $$? What do you want to end up with HP wise?
With regards to your question about how hard is it, the boards are full of ppl that have swapped/exchanged/rebuilt their motors in their driveways using nothing but hand tools, jack stands, and a rented engine crane (including myself).
So if $$ is really limited, get a salvage yard motor (car-part.com) and call it a day. However, expect that the Cobra specific parts such as intake manifold will cost more than you think.
Again, IMO it is vital that you list your goals in order. It is your project and your $$. The best answer will come to you once you have an honest understanding of your goals and abilities.