Rick,
There is no pad. Give Scott a call at West Coast Classic Cougars. There are a couple types out there and he can steer you to a quality top.
The windows have to be removed and it is a good time to replace your window gaskets. The rear seat needs to come out to get to the rear interior panels. The carpet scuff plates need to come out also to get the rear interior panels out. The rear interior panels need to come out to get at the nuts that hold the trim to the car that finishes the top at the quarter panel.
This job is kinda a big one. Be very careful with the drip rail trim. And be very careful with your front and rear window trim. Repo stuff is crap and the originals are easy to bend up. Some of the Mustangs had a chrome trim strip in the bottom of the drip rail. It is held on by 2 rivets on each side and is very fragile. You need to fit the vinyl top securely down to the drip rail and up its edge to the top of the drip rail, but not over its edge. The trim will not fit over the vinyl if it is on the edge.
I just did one a couple months ago and it is very time consuming to get it correct.
Anyone that says you do not need to remove the above is doing a half ass job and you should walk away. Do not shop on price, and find someone who knows all of the above.
Rob