As for thunder 2, you can remove it from your bar but what I would recommend is using a macro for it with Thunder 3.

/micon "Thunder III"
/ac "Thunder III"
/ac "Thunder II"

Least that way if you get sync'd down you can still use Thunder 2 in the case of a proc but you still save up a slot. Will attempt to cast Thunder 3, if it can't (because of MP or level) will cast 2.