Check the usuals. The '97s were pretty solid and I can't recall them having any major issues.
Make sure the trans shifts in and out of each gear ok - want to verify the previous owner(s) didn't beat it to hell from power/speed-shifting or racing with it.
Does it have a lot of mods or is it fairly stock?
Obviously, a no brainer - but verify via the VIN that the vehicle is an authentic Cobra (can call Ford SVT at 1-800-ford-svt during normal business days/hours to inquire). I forget what the "Cobra" engine code is on the VIN offhand...
Has the previous owner ever cleaned the IMRCs ? They tend to get gunked up and a thorough cleaning is probably in order for a 13 year old car. This is more of a maintainence issue though, but just be aware of it - you want to make sure the IMRCs are still functioning and opening up at ~3250rpms or whatever.
Run a search on "IMRC cleaning" - there's a link to a PDF document floating around in past threads that will outline all the steps to remove the intake and properly clean the IMRCs with a little bit of elbow grease. Makes for a good weekend project.
Wouldn't hurt to run an engine compression test on it prior to purchase, just to confirm the health of the engine.
Other than that, there's nothing really "unique" as far as items to watch out for go - you probably already know most of the ins and outs of this body style since you had a '98 GT in the past.
Keep us posted...