Trying to remember whether this applies to my G/S or the R65 output seal cover. Think it is both.
Once the nuts are off, sometimes the cover doesn't want to lift and you shouldn't try levering with a screwdriver etc.. There are two threaded holes, I think at 1pm and 7pm, probably covered in oil and muck. Takes a 5 or 6mm bolt. Thread them in and tighten, it will lift the cover off.
Although BMW fiche showed a paper gasket under the cover, both my G/S and the R65 didn't have one there, so I kept the status quo. Just used some gasket goo.