Two problems related to clutch pedal/linkage have been reported for the 1999 Mercury Cougar. The most recently reported issues are listed below.
Loud grinding noise from the manual transmission occurs when car is down shifted to first gear coming to a stop, or shifted to first not being at a complete stop, the shift lever "pops out of gear" and admitting a very loud grinding noise. Preventing this would be coming to a complete stop from neutral, then after stopping completely proceed to engage clutch and put car into first gear. First gear sometimes hard to shift into, might be a shift linkage problem. Sounds like the manual transmission grinding with a loud winding squeal.
Intermittent engine racing to 3000-3500 rpm, when clutch is engaged, which lasts for approximately 10 seconds and intermittent overdeceleration (as if the brakes were applied) that releases when the accelerator is tapped.