1997 to 2006 hardtop should fit fine.
No.
on the transmission
Yes, they are both TJ's and it should be a match.
Mopar ATF+4
Yes, it is laminated glass.
No.
There should be some screws and nuts and bolts.
One can buy a brand new Jeep Sahara from the Jeep dealership. One can buy a used Jeep Sahara from Kelley Blue Book. Another place to buy a used Jeep Sahara is on Auto Trader.
Jeep has a Wrangler Sahara.
The Wrangler X is a trim model below the Sport. Wrangler, X, Sport, Sahara, <insert specialty trim package here> i.e. Golden Eagle The Sport typically came with both soft and hard top, some Sahara available options and other minor trim differences.
3.07 or 3.73 to 1. Could be either.
97 thru 03 should fit, all TJ's