In the above post Handler Guy Bruneau over at the Internet Storm Center has a post that talks about his upgrade from Snort 2.8.6 to Snort 2.9.0.2, and some tweaks he found for DAQ.
Those of you preparing to upgrade or experiencing problems with upgrade to Snort 2.9.0.x may want to take a look at his post and see if it solves any problems for them.
Thanks Guy!