749R comes with loads of stuff the 999R don't, different shock, rocker and suspension action and frame/forks have adjustable offset. Reasons for this are Supersport racing allows less changes from standard so it has to be homologated by a production run, 999R can have quite a few changes for WSB and BSB but not as many for AMA. i'd heard rumours that the 749 won't change for 2007 and that possibly the R will be identical, not sure how true that is though
the clutch problem is almost certainly the slipper, i've removed mine from the 999 as it slipped too much in town and made the bike a pain to ride and every so often you'd end up stalling it. the 2 stage effect will be the basket starting to open the plates as you start revving it cos the spring is worn then the pushrod takes over giving a notchy feel. it probably needs a new slipper spring.