Comparing a 993 engine to an LS-1 in a kit car ...............
The 993 engine will cost more. The 993 engine will have less horsepower. the 993 engine will have less torque. The 993 will weigh almost as much as the LS-1.
Other than that it sounds like a really good idea
About the only things the 993 engine does better are sound and feel.
As far as factory five having a good reputation, cough cough I don't think so.
Maybe now they are great but as little as 7 or 8 years ago they built the pep boys or walmart of cobra kits. Biggest POS on the market. An entire chapter out of a Cobra book I have ("The Complete Guide to Cobra Replicas") was dedicated to explaining who the factory five cobra kit should not be purchased and why, specifically quality and safety.
You could always call Cobra City in Orange and ask them what they think about factory five. they won't even let one on the lot.
You see around that time I was very serious about building a cobra.
My wife saw how much it was going to cost and said "why don't you get an old Porsche and fix it up like you used to do when you were younger" and the rest is history.