I think the rarest of them all was the 89-90 Cougar XR-7 SC with a manual. I think they made like 3,000 at that. Those were pretty sweet.
The 89-91 T-bird and Cougar did have a lot of problems though. I should know, I sold the parts for them
http://www.fordmuscle.com/archives/2005/12/CougarXR7/index2.php