Welcome to the madness Jon.
If building yourself is the first priority, FFR is a good choice. If cost is also a high priority, and you don't mind having used parts, FFR is probably THE best choice for you. FFR is unique in that there is such a large customer base, and a large online community, and you can easily get help on your build if you need it.
I was planning to build an FFR myself, strictly for the purpose of keeping cost down. I don't have much experience with car builds. I then found a new company called Carcepts that follows the same donor principle as FFR, but also builds complete turnkeys at a very reasonable price. Their price is so good that I wouldn't save much to build it myself, so I decided to buy a turnkey from them.
ERA and SPF are two of the premier Cobra replica manufacturers. There is a HUGE price difference between them and FFR. I know at least ERA offers kits. If you plan to put in a 427 or any other new parts or performance goodies, FFR loses its price advantage. The components FFR includes in their kit are as good as anybody. Replacing the donor parts becomes expensive. Other makes include nifty components by default, and you pay less by purchasing them together with the kit. Examples: B&B, Shell Valley, Unique, Lone Star, plus many others.
There definitely are differences in the bodies of the cars. Some manufacturers offer wheelbases beyond the original 90", usually to allow for more cockpit room. In my experience, the front ends of most Cobra replicas look the same. The rears is where you see a lot of difference. The flare of the rear fender can vary dramatically. The FFR 'perky butt' means that the rear end sticks up a bit. Looking at the car from a profile, it seems to me like the mold was bent up a bit at the rear wheel well. The shape of the rear fender is how I can usually differentiate different makes, and this is totally a matter of personal preference. It took me at least a year of looking at pictures of the cars to get familiar with it.
From ERA:
profile comparison
There's nothing wrong at all with the FFR kit setup. The only drawback is having used parts. I understand that FFRs hold their own quite well in competition. You don't see
oil coolers on FFRs because most of them are built with 302s that don't need an
oil cooler.
As far as using Fox-Mustang components, if you'd want to use the gas tank, radiator, solid axle rear, and front suspension from a Mustang, then FFR is right up your alley. Otherwise, you can use the same components in most any Cobra replica.
If I were to recommend a Cobra replica for you, I would never include ERA, SPF and FFR in the same category. You can make a great car with any of them, but they are very different. FFR only makes kits. They stick stuff together so it fits in a crate, but that's it. ERA pre-installs most everything - that's part of the reason why it's more expensive. ERA only offers IRS. If you want to build an FFR at the level of an ERA, it's gonna cost ya. If you're looking for flexibility, and you want to do it all yourself, and you don't want to spend $50k-plus, choose FFR. If you want a prestigious, accurate, best-component, expensive car, choose someone like ERA.
Go to places like CobraCountry to learn about all the different makes. It sounds like FFR is right up your alley, but don't make a decision until you have thoroughly considered your options. Like I said, it took me at least a year before I could even tell the difference in the body shapes. A lot of FFR guys build with 17" rims, which is often a tip that the car is an FFR.
Good luck!