Just want to verify....will a hardtop off a 2006 fit on a 1999? Also, I've only ever had a soft top on my 99...will I need some kind of extra hardware to convert it to hardtop?
Yes, as long as you don’t have some type of after market header attached to the top of the windshield you will be good to go there.
Again yes the sides just bolt down. Depending how old the top is and how it was taken care of a new gasket kit may be in order
Your rear window may break its seal when you shut your front doors as the tailgate vent is missing, not a problem as long as you push the window back down to seal it in heavy rain after shutting the doors.
If OP's Jeep is a factory hard top model and wants functional rear wiper/washer and/or defrost, he'll have to buy or make a conversion pigtail harness. If OP's Jeep isn't a hard top model and he wants full-features, he'll need the washer solvent jug w/ dual pumps, body harness from pumps to switches, to back of tub, pigtail harness, and the switch bank. OP might be able to find a Mopar retrofit kit, otherwise it's finding used parts.