New2Jeeps42

So guys i found a 95 Cherokee Country, 160 miles on it, great interior, in need of some looking into.
I took it to my mechanic and he replaced the brakes, rotors, a wheel bearing, welding the funking exhaust back together, tuned it up can changed necessary fluids and filters, and made sure the 4x4 was working and functional.
Its a really nice vehicle, however ive noticed a few things.

Firstly it needs shocks, which i have already got, and have an appointment to get them put on later this week. When i go over bumps i hear and feel in the floor a bit of a clunk/knock and in my 87 cherokee, that was bad shocks for sure. My brothers car recently broke down and i had to tow him home and i think that has exacerbated the shock problem, also i had a leaky tire (add some air every week or so) and after the tow it wont hold air at all. Is this something i should have figured would be stressed by a tow? or is the tire thing just a random occurence?

Secondly theres a intermittent rattling, loud on start up, randomly during idle and a little when going over bumps. My instinct tells me (from driving tons of cars with exhaust problems) that it is the exhaust rattling against something, or CC elements or something, it is a haggard exhaust system.

Thirdly when i start it, it clunks, almost like a muted backfire, and feels like a stronger version of the rattling that happens on idle.

and fourthly and the real input im looking for here, is on the rust that is on the top of the windshield/roof area. it appears to allow seepage into the interior, and when i first got the vehicle i noticed that the overhead console/compass thingy was soaked. it dried out, but just the other day in a rainstorm if conked out. then came back and said it was 108 farenheit outside. which it wasnt. Should i just grind off the rust and repaint it and cram some sealant into the windshield? if so what product should i use?