The drivers side quarter light frame was badly rusted at the bottom around the window brakes mount. However, the rest of mounting frame is in reasonable condition - so worth repairing. As the repair will be covered by the new rubber seal it doesn't need to be pretty, just strong enough to last.
Replaced the bottom window clamps as they were wafer thin due to rust.
After much trial and error here is the passenger side door windows back in - there is only about 2mm clearance and you have to put the main window in before the quarter light.
I've used double sided waterproof tape to secure the quarter light glass - not sure if this is up to the job.