Yes the sunroof is one. I could tell from a number of ads when I started to look at the Cougar that it is a problem spot to check carefully before a buy.
In my case I avoided that problem by getting one that had no sunroof at all.
Correct, the 1999-2000 Cougars had major problems with the alternators. Read the guides and recommendations here about the problem. We have replaced three in our 2000 and it is still not right. We have had no such problems with our 2002 though. Seemed to solve the problem in the last model year.
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