The pads go in between the steel frame and the vinyl top. You'd be retarded to put a new top on w/out replacing the pads. The new top would just wear out quicker, and you'd only save $50.
The frame cables I'm referring to are riveted just behind the header and run along the sides of the top to about halfway down the back window. They keep tension on the top right/left and fore/aft. They're also pretty easy to replace. You have to drill the old rivet out, and put new rivets in, but it was actually a lot easier than I thought. This is another easy thing to replace while the top's off.
I actually didn't replace my weatherstripping... The full weatherstrip kit from mustangsunlimited.com was about $150 I think, and mine suprisingly still works fine. It was a bit dirty, but functional. My new top (although I still have a few wrinkles behind the backseat windows...) is water tight. My old top only stopped rain drops bigger than golf balls... ;-)
Just curious, what was your quote like?