I think the simple answer is that, apart from the paint jobs, the S is blacked out and has the 110B engine whereas the "standard" slim isn't blacked out and has the 103B engine.
The slim and the slim S are TC engines, so discontinued now. There's not yet an M8 Slim S.
The new M8 Slim has blacked out forks, the 107 engine and is about a grand more than the original Slim (so about 2 grand less than the original Slim S)
From what I've seen, HD have managed to make the M8 run ok without having to do the stage 1 work (the M8 114 seems to have the same performance out of the crate as the 110 with stage 1).
I love the look of the Slim S (probably from years of watching M*A*S*H*) but with all the upgrades the new bike has a lot going for it.