I haven't pulled one myself, but I've watched it in person many times. If you aren't worried about the glass breaking (since you have cracked glass, it will most likely crack more when you pull it out), it shouldn't be too hard.
The big problem with rust in there is when the glass guy pulls it out and scratches the paint off in those corners, then just slaps the window back in over the bare metal. Water gets in and it starts rusting.
You'll probably want some cheapo glass suction cups, Harbor freight sells to different types, dual cup with handle, and a single cup with handle. I would think the dual cup would work better, but both do a good job. I use them for removing large acrylic sign panels from backlight sign boxes.
Cutting the seal will be the hardest part, You will need a really stiff wire hangar to poke through the seal and into the cab, with something like a guitar string or other really strong metal wire. You'll use it like a sawing motion all the way around to cut the seal away from the body.
With two people, use the suction cups, pull it away and throw it out. Then you can spend the next few hours cleaning that rail all the way around! I would definitely seal it with some sort of paint or other rust preventative once you're done.
If you see holes, you're gonna want to braze them shut with an oxy-acetaline torch and brazing rod. Check behind for any wires or soundproofing so they don't catch on fire!
If the holes are too big to braze (mine were literally pinholes, super-small and easily brazed shut, but the body guy brazed a metal strip in there too just to make sure it was all good), you're gonna need to form a small strip of metal to repair it.
Call around and see who will pull the window, then come back to reinstall later, might be a few bucks more for the guy to come back a second time to install, but having them do the work and take the glass away would probably be worth the cost!