A small but significant update this evening. I spent an hour putting in the passenger window with new seals and weather strip.
Instead of mastic, I used some draught strip which should do the job nicely.
Sadly, the first scratch also happened. I'm sure it won't be the last, but it's good to get it out of the way. I protected the lower edges with tape whilst fitting the window but not the window surround.
Thankfully, Ben provided me with a touch up pot which will come in handy.