I have had Superformance and Backdraft "factory built" cars as well as B&B, Hurricanes, Kirkham and RCR kits. First, the ride difference on the IRS is imperceptible. You will not feel the difference unless you are on the very edge and driving the the sh!t out of your car. I have had quite a few of both and the ride is more about the springs, shocks and tires. The IRS is cool and you will get more for a car with it, most of the time. At least most of the higher end cars come that way so it is the standard. The 9 inch vs 8.8 is not a big deal unless you are a serious drag racer. Your tires will spin before you put enough torque on the rear end to break anything. That is the easiest of your questions. Next is the fuel delivery. You will have more trouble free miles with a Holley, vacuum secondary, electric choke carburetor. My fuel injection cars ran awesome but it is not the same as your daily driver. It takes time and money to tune the injection and even then some people never get it set right.
Know for the harder question. Kit vs Factory build. Let me first say that just because it is factory built doesn't mean it is right. Don't believe the commercial they will try to spin. Ask to see numbers for the bump steer,corner balance, wheel rate, etc. (if thats important to you). As an example, my Kirkham cobra and my Superformance GT40 would fail the bump steer test but they both felt great to drive. I didn't realize what a correct set up felt like until I built the RCR GT40. I had it set up by a professional race team. It didn't come setup because I built it but it was super adjustable. You can correct or set up most of these cars but don't think for a minute that they come with the optimal settings already dialed in. If a manufacturer doesn't have the numbers to show you, assume that it isn't set up and will require adjustment. As for parts, that is pretty subjective too. Backdraft has BMW stuff but is less adjustable than some of the others. It is also more expensive to service than Ford parts or widely used aftermarket stuff. It does have an awesome ride, very smooth. The kits can be built with the parts you choose so if you go cheap, thats what you get. If you get the factory built standard stuff, it is going to be standard stuff but upgrades are available. I don't think you can make to many assumption when you are looking at cobras. The first thing to do is very specifically outline what is important to you. Then come back to the forum and ask the questions but always look at what car the guy owns when he gives you an answer. We are all partial to what we drive or we wouldn't have bought it. I hope that helps.
Here's a link to my build thread for my latest project with Hurricane,
Hurricane HMS2002 build thread part II
Send me a note if you have any questions you want to ask off line. I'll be happy to help.
Dean