Rear window, no problem - about 10 bolts and it will ease out. A little butyl and bolt it back in and you would have replace the solid glass with a slider. Door glass, again no problem - 2 bolts, drill out 2 rivets and its yours - you can substitute a 3/16 bolt and nyloc nut for the rivet to reinstall. Super cab windows are even easier, they just unbolt.
Windshield - call the pros.
Removing a windshield at a wrecker is a two person job and challenging one at that. You need a length of fine wire (guitar string), couple pencils (hardware store ones are better than round ones), and bunch of popsicle sticks.
You thread the wire between the windshield and cab and wrap around pencils. Then, like lumber jack of old, persons inside and outside alternate pulling wire in and out while working their way around the windshield. Popsicle sticks are used to hold windshield out as you progress so it does seal back in.
Care must be taken not to saw against windshield (and break it) or against frame and damage the paint.
With both windshields out, you clean old glue off your truck and apply new. Then, install the replacement windshield, duct taping it in place for 24 hours while the glue sets.
As it would cost me $50 for windshield (assuming I could find an undamaged one), $20 for the caulking/cleaner/paper towel/etc, and at least 3 hours of my time and a buddy's*; the $175 for my glass guy to come and install a new windshield in my driveway is worth it. Note: the $175 is Cdn, USD price would be about 75% of that at current exchange.
And getting it done by a pro guarantees not leaks (if it does - they fix it).