Hi Sam,
The rubbers will be O.K. just peel them away prior to opening the track buy some rubber silicone spray from Halfords and give the inside of the rubber where the windows slide in a good spray and leave for a while. You can be quite brutal with the track I not only opened it out I pushed it towards the door frame too. Be carefull opening up the track one slip could be a dent on the outer skin of the door.