From what you've said it sounds like yer motor may not be broken in yet - it's a night and day difference. Everything you described sounds exactly like mine before it finally stopped acting silly and began to run properly.

If not, if you have well over 200 miles on it and it's still vibrating like **** - perhaps it's not mounted as securely as it could be? Excessive vibration can cause fuel frothing in the carb making it run worse, an annoying cycle if there ever was one (mine took over 300mi to break in, I blame good oil).

Stuff to look at;

plug coloration and fuel/air mix
air leaks
properly sized gaskets*
centered rear sprocket

It does really sound like yer motor is just still "too new" though, that's an easy fix


*The center hole in these gaskets is usually far smaller than their respective manifolds, make sure the hole is as big around as the inside diameter of the pipe it goes to.