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I am pretty sure they are slightly different but I think you can get them to fit with some shortening of the runners but it has definetly been done.
yea its a pain cutting the runners also some of the holes have to be redrilled at the front as there in different places if i remember right . just change the glass if at all poss and leave the frame
They are different indeed. I have replaced both of my cars' sunroofs with S2 sunroofs. Not a straigth forward swap at all. One needs to use half the parts of the S1 and half hte parts from the S2 to make the glass fit.