well ...bass on the MKS is different, i wouldn't say stronger....maybe a bit softer and deeper.....while JP6 has some sort of punchiness that i can get from MKS with some Eqing and compression. I think that MKS needs more processing than JP6 to sit in the mix....but they both need some processing to get the best out of them....
It is really difficult to describe in words what are the diffs between them....
I think that the clicky sound is present on all Rolands of that era , don't know why....it doesn't bother me....
no you can not run VCOs through up/low outs, but you can do some interesting layers with different sounds instead ......
hope this helps a bit....