Hey Rick,
Welcome to the forum, and possibly welcome to the world of Cougars.
Stuff to look for with the car will depend on age and mileage. Obviously, all the usuals, and you should get a feel for the car first and drive it if possible because you need to know if it's the kinda car you can drive and put up with.
A good service history is paramount. These cars can be difficult to get parts for, and a lazy previous owner could cost you big bucks further down the track. Parts are not cheap.
Known problems include alternators failing, door actuators failing ($600 per door), sunroof trouble (mainly in the US, and mainly on the older models). Reviewers would often complain that the front seats were not supportive in the older models as well.
Cougar-Boy's opinion of the model change is purely subjective as I feel the 01 shape was an improvement over the older! Though, I will admit the 99-00 models look more cat like from the front, I like the aggression of the new bumper on the 01's, plus the interior rocks! But, the older models are easier to lower because Ford changed the rear spring setup in the 01's.
Bodykits will be an absolute pain to buy now... it was expensive when I sourced mine, so unless you have a lazy few thousand lying around for supply, spraying and install, you might be better to concentrate on having a nice low car, with some decent wheels a bit like what Mark (pcperfection) has done with his.
Sought after Cougars are generally the 2000 model Eibach edition, but these will fetch higher dollars, or a low km 00 or 01 model in good condition. Most will be out of warranty now, unless the owner was prudent enough to extend it like mine has. Leather interior is a nice option if you can get it, and the manual is the better transmission
All up, good luck, and don't hesitate to ask any questions!
Dan