Did you do the mods (add the pipe and jetting) before you noticed that it was not so smooth. It could be the pipe that took the smoothness out of it. Correct me if I wrong, but you could try a flywheel weight to smooth it out. Just my .02
Most of our group were flying front wheel high (SCARY HIGH) after we rebuilt the jumps bigger. The things that helped were:
stiffen forks, this helped the most- I think there is some rebound thing from hitting harder; make sure your handlebars are not too far back- get some weight on the front; and practice, practice, practice.