Weren't the 03 to 05 V6s 4.0L OHCs? If you had a 3.8L Cougar with 200K on the clock, you were one of the lucky ones.
Cruise control shouldn't be that big of a deal. Most likely the wiring is already there for the factory controls. You'll just need the VSS and a couple of other things. A good J/Y donor would help immensely. I like CC on the big roads too. I get better mileage in my pickup or any other car because I'm not peddling it to keep up with or get out of traffic.
I have no issues with carbs. A good properly tuned carb can achieve good performance and fuel efficiency. The problem is the maintenance they constantly need. I don't care much for Quadra-bogs but I do like spread bore carbs. Little bitty primaries for pinching fuel and great big secondaries for taking care of bidness.
As I was saying earlier, I'd love to see a late model OHC V6 in a Fox Mustang. My wife drives an '06 with the V6 and while it's not V8 quick, it's still no slouch. Rated at 210hp, it's not far off the mark of 5.0L V8s from the Fox era.
The downside to all this cool swap talk is that outside of the common turbo 4 build ups ,and V8 transplants, none of the other options are easy. That being said, they'll also be more expensive, time consuming, and difficult. Now you have to weigh out the options. Is the effort worth the result? What do I gain and at what cost? Do I really like the car that much?
I dunno.