I'm new to the Pantera world (still looking for my first one to buy), but I've been in the late model Mustang game for quite a while. The first response to anyone asking that sort of question is, what exactly is your end goal? Give us the horsepower level you'd like and the amount of money you would like to spend. Remember the golden rule of engine building, choose two of the following...fast, reliable, inexpensive. You can make it fast and reliable, but it won't be cheap. You can build it fast an inexpensive, but it won't be reliable...etc etc :-)
But, just slapping on an aftermarket EFI system on your 351C won't give you a huge jump in performance or reliability. Actually, a carburated engine will make more horsepower than EFI, with all other things being equal. The benefits of EFI are mainly drivability, it will idle great and the a/f ratio will be perfect throughout the powerband. But don't fool yourself in thinking it won't break down just because its "modern". In fact, you'll add in all sorts of new variables that will cause your engine to malfunction. And, if you're really that concerned about getting good mileage, buy a Honda (j/k). Carburation is SO simple and easy to work with. A properyly maintained 351C with a vac sec Holley and electronic ignition will give you years of reliability. The one place where fuel injection excels GREATLY over carbs, is when using a power adder. I'd LOVE to see a 2003 Mustang Cobra engine in a Pantera. How does 400rwhp and 100,000 miles of reliability sound?
If you have your heart set on EFI, I would defenitely go the Windsor route. There are lots of proven combinations available. The Ford crate motors are great, I have one in my Mustang. The best part is you can use factory equipment to set up the EFI, nothing exotic or custom. Any late model Mustang shop can work on it or diagnose problems very easily. These guys are probably the best at getting EFI systems into early model cars...
http://www.windsor-fox.com This, of course, is just my opinion when dealing with Mustangs. Someone else might have better, Pantera specific answers concerning EFI swaps.
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1985 Mustang GT: 351W, Griggs, Baer, etc etc
2001 Saleen S281
1970 Torino GT Convertible: 351C