The 'capping that secures the window-frame to the bulkhead'?
Not certain what you mean, you aren't referring to the hinges (or dummy hinges) are you?. The windscreen-frame is secured to the roof by a line of bolts and to the bulkhead by the hinges, shouldn't be anything else holding it on. The hinges are unbolted from inside.
The bulkhead top-rail is a very common rot-spot, if it has gone (you will get an excelent view wth the frame off) then you have to consider if you want to save the bulkhead or go for a replacement because let me tell you now, for all the rot you can see it will be a lot worse inside where you can't see it. Be brutal, have a really good poke around and while you are at it look at the top of the pillars as well.