well... for future ideas, instead of using string, use those little pins made for making dangely jewelry. You can get them at walmart.
As for securing what you have... if you have crimp beads you could slip a crimp bead on and crimp it which would hold everything in place.
The sad thing about nots is there habbit of coming untied when you cut the extra strands off. Drives me up the wall. You could probably trim those a little shorter without problem, they honestly don't look bad with the string hanging down though, kind of a cute touch.