Ah, the infamous clutch chudder. My '02 does the same thing and I've been told that it's annoying and can be fixed by changing the clutch basket but won't cause any harm.
As far as the rough running is concerned make sure you have the throttle bodies synched (do a search and you'll find everything you need to know), this is something you can do. Your bike is also probably running lean which can cause the problems you're experiencing under acceleration. There are some fixes available (Yosh treatment, PCIII, Dale Walker's DFI...).
As far as the leak on the left side goes, mine did the same thing... once. I wiped everything up and started keeping an eye on it and it's never happened again. Not sure what that's all about...
Look into the above things and enjoy the new ride!
Gone but not forgotten:
Blue 2002 Vee