I removed my W123 rear window (84 300D) and reused the rubber seal as mine was still pliable. So I can only be general.
Doing it myself I had harborfreight single and a double suction cups with handles and found them invaluable for holding on to the window and to position it.
Lay something like a well padded blanket on top of the Trunk so that if the Window slips it does not get damaged. Sort of the same where ever you plan to lay the window while you do other work.
In my case I had rusted through holes under the rubber seal I had to deal with. That delayed the job and means the window is going to be out of the Car for a longer time then planned. That means the need for a Tarp and even if your Car is in the Drive Way it could attract thieves.
Besides the thief issue I have found the local stray Cats have gotten under tarps and inside and took a nice pee inside.
I am not sure what is here for your specific vehicle: Repair Links
Fast navigation
http://www.peachparts.com/shopforum/diy-links-parts-category/146034-fast-navigation-do-yourself-links.html
These sites if they still work may have a service manual for you to access.
http://forum.w116.org/register/
W114/W115 Manual and info site
Mercedes-Benz Model 114/115
http://eva2.homeip.net/W115/program/Chassis/35-010.pdf
Blog Site W115/116
Restoring "Marlene Diederich": My Mercedes Diesel Rebuild: Service Manuals for the Mercedes W115 300D