Window track and body trim nut help needed

Id like to start putting the windows back into my 66 Dart. I have everything removed from inside the door. The questions I have to start with are do I install the door handles and linkage or the window regulators and tracks? Also do I need to put the window wiskers in place before the window is installed?

Also I hope to start putting some emblems and trim back onto the car ad was wondering what you use inside the nuts for im guessing a sealer? Originally they had a rubber type material inside the nut. Of course that dried up and fell out long ago so I will need to replace it.
Hoping to make some progress here in the next 2 weeks.
Thanks Rod