William, welcome to the madness. I'm sure there will be lots of input for your questions so I'll just throw in my 2 peso's worth.
Yes, a Chev motor will probably be a red flag to some but it is your car- do it the way you want it. With 25 years in the service, you've probably got pretty thick skin.....
Two things to consider- the Chev engine may kill resale value unless you find just the right buyer when the time comes (and it always does eventually)- and be sure that whatever kit you choose that your engine choice is supported by the manufacturer so the proper mounts and space is available for the engine to actually fit in the compartment and connect to everything properly- headers, transmission, engine mounts, radiator connections, etc... not all kits fit all contingencies.
Another point- the Big Block chev and the 385 series Ford engines (429, 460) are heavy engines. For purposes of a lightweight car like a Cobra, be sure you have the proper set up to handle the extra weight up front and be prepared for a car that may or may not handle like the sports car it is supposed to be. IMHO a small block or 427 FE is a better choice due to weight considerations. If cost is a factor, you would be better off with a well built small block. You can easily get more than enough horsepower from a good stroked small block in a smaller, lighter package to wet your pants and that of your passenger.
Pin drive or 5 lug? Again, may be a cost consideration here. Much cheaper to go with the 5 lug wheels, but depending on which replica you buy, it may or may not come with pin drive mounts. Then the decision is made for you. If cost isn't a consideration in this case, the pin drive are more original looking and definitely have that cool factor. For a new set of pin drive wheels you're looking at $1600-$2,000 plus the cost of the adaptors if the car doesn't come with pin drive already.
Good luck with your search. Which replica have you been looking at the most? Some are supported better than others but there are lots of great manufacturers represented here.
Bob