Well.. firstly. I am glad you are sticking with the mustang and not scared away from it. If you are looking around for a cobra, try and get one with just the basic mods and nothing to extreme. Mods like cold air intake, shifter, exhaust and subframes are nice. pulleys, blower swaps and drag setups I would stay away from.
If it has the stock F1s on them is a good sign, specially for this car with about 20,000 miles. That would give an indication that the previous owner kept it pretty much stock and wasn't into replacing tires every 10,000 miles.
A hood blanket that is untouched will also be a good indicator that the car wasn't modded and then returned to stock... it's almost the first thing we do to the car.
Also, headers on a car would also indicate it's been heavily modified. They are a real pita to get on/off, so if the engine is stock and there are aftermarket headers on there... there is a chance there were other extensive mods.
This is all not to say that a modded cobra is to be avoided like the plague, but if someone tells you it was never modded and price it accordingly, it's nice to point these things out.
If the car has a pulley/tune or other more serious mods, find out if the car will be covered under warantee and get it in writing. You put the wrong gas in it, or it blows smoke, you want to be sure it's covered. That being said, there are alot of modded cobras that are done safely and fun as he11.
As far as the issues that the cobras have/had, there were a few. But none of them are/were show stoppers and can be corrected under warrantee without questions asked by the dealer. There was a cylinder clearance issue where the car would develop a ticking. It would be most audible by going into a drive through window with the drivers window down. This is not to be confused with the noise on cold startup that some engines have which are built with such tight cleanaces.
Have the dealership pull up the Oasis report from their system. This will tell you what work was done on the vehicle prior and during ownership. Carfax reports are also a good source for information.
Nothing can replace a test drive. I don't mean drive it around the block, but take it on a highway, give it full throttle and let the car tell you how it's doing. Test drive several cobras. This will give you an idea what is "normal" and what is not.
The clutch is very heavy. But they are not all sprung the same after use. Try to take the car over speed bumps and listen for creaks and pops.
The fit & finish on this car is going to be the same as your regular mustang. the paint, interior, body panels,... etc, are the same quality that comes with the V6 and GTs.
The drivetrain is what makes this car stand out tho and it's what I wanted most. Once you hear the supercharger whine, it's all over for you...
... you're hooked, and it's all worth it