Just doing the dry build on my Series 2 Winter and the back edge of the side panel is hanging below the tail of the frame, frame rubber and buffers are fitted. Now, I know these aren't the original panels, but is there a way of lining them up better to get an even gap along the rear footboard or lining up at the back?
Welcome to my world... I've been dealing with this issue since I ever started with series 2 obsession. The truth is you will need to do as you yourself suggested and try first with rubber. Then if that isnt enough, fettle a bit with the edge of the sidepannel & the frame itself.
A quick change of panel rubbers seems to have sorted it...
Casa rubbers are crap, as are the SR ones, but for the second time now, the ones that come up trumps are ScootRS