I spoke to several lawyers about my situation and they all told me I was in trouble. Since I did not have the certificate from the state at the time the probation officer noted my plants I would be going to jail.
Coolboarder: I assume you did not make copies of the papers you submitted to the state? I was under the assumption that if one makes copies of these papers along with a certified copy of the sent letter, then that would be enough proof to begin growing or buying - especially given that the State is taking a long time to process all the applications they are getting. If you did this and these lawyers are telling your otherwise then .... hmmm...