Tough to answer all your questions completly in one thread. But if you do some more reading here and on other boards, you'll get a lot of good info.
What engine? That like asking "What color?" The sky is the limit, do whatever makes you happy. SBC, BBC, SBF, BBF, Ford or Chevy stroker, Dart block, Man-O-War block..... They all work, and work well.
One of the biggest bangs for the buck these days is Ford's Coyote crate engine. That's a screamin motor for minimal cash (considering what you get). They perform really well on the track, too.
Personally, I think the FFR chassis is the best you can buy or build for <$50K. It is a
really fun track car.
MkI, MkII,. etc refer to ongoing changes and development in design. They're up to MIV now. The new bodies are molded from Dick Smith's #98 car - so externally it's a very accurate copy.
You don't need to be a certified mechanic to build an FFR. It helps if you're a certified car nut, though. The FFR kit is very well designed, and you can almost build the car with a screwdriver and a crescent wrench.
Superformance makes a good car. IMO, the chassis isn't as good as the FFR's - but it is still very very good. It's one of the heavier kits on the market. It comes as a roller, and ready for the drive line. It even comes painted, with the full interior installed. A friend of mine had his Superformance roadster delivered on Friday, and he drove it to the DMV for inspection on Monday.
The ERA is also very good. It's also an exact copy of an original, inside and out. If total originality is your goal, ERA is the one to choose.
Third party support is also important. How many non-kit parts can you find for your chosen car? How many "upgrade" or alternate components are available? FFR has some of the best third party support on the market. And they should, since more than 1/2 of all cobra replicas on the road are FFR's.
I put after sales customer support very high on my list before buying nearly anything. If I have a problem, can I call or e-mail some one and get a response in a reasonable amount of time? I think ERA probably has the best reputation in that area, with FFR a close second.
FFR has two forums dedicated to that kit. Tons of information on problem solving, good ideas, bad ideas, news, etc. The FFR owner network is huge. If you get stuck on something, you can usually find the answer already posted on the forums, complete with referances, pictures, and diagrams. If you can't find the answer, ask the question - you'll usually get an answer back in no time. Usually. Every now and then I manage to stump the experts, and then I have to figure it out myself.
Try and find a Cobra replica to look at, touch, feel, and get a ride in. I'd be willing to bet you can find a FFR to look at fairly close to your home. Try and look at other kit's too. They're all Cobra replica's, but they're all different. They all have their good and bad points, quirks, and personality.
But, that's just my opinion. I could be wrong.