I have an 08, same bike as the 09. Same basic mods you have, fmf pipe/header, ais removed, and all the free mods. The exhaust made an amazing difference in performance. You should remove the snorkel from the intake if you haven't done that yet. It's under the seat by the battery. The suspension was dangerous stock. Why they sell a bike set up so soft amazes me. I had ESP revalve/spring for my weight/skill and desert riding and it transformed the bike. Lots of companies out there that can do similar work. I don't see the point in changing to yz suspension. My sons revalved yz450 suspension works no better than mine now.
we actually didn't do the snorkel, based on this comment from the FAQ (http://www.thumperfaq.com/airbox.htm):
"The snorkel can be easily removed to improve airflow but the performance gain is minimal as the airbox is still quite restricted by the battery. "
did you remove the battery as well, and hack the airbox or just pull the snorkel?