Is it a CVPI? To check, look at the VIN if possible and see if it has P71, if it does, then the tailshaft is too long. If it is P73 or P74 then it should be fine. Both should have the same thing for the speedometer, both are 4R70Ws, no need to change around the wiring, I don't know about the MLPS and the TCC, should be a direct swap both engine and tranny.
Some of the intake stuff will need to be reused from the thunderbird like the fuel rails, but since they are both already composite intake cars, should be an easy swap.
97 Mark VIII LSC/Silver/Gray leather
97 Cougar 4.6 Sport/White Opalescent Tricoat Metallic /Gray leather down but not out?
89 Cougar LS 3.8/Oxford White/Gray velour/HG need replaced AGAIN
00 Grand Marquis LS/Vibrant White/Gray velour
63 Falcon 302/black and rust/shed isn't moving
82 F-150/Oxford White/dumb VV carb doesn't pass emissions