confusion with FMLA, STD, complaint ag. Boss

[TNleia]

I have several issues here. I'm in Tennessee and work for a company that is held to FMLA laws. First, about 3 years ago I was diagnosed with Ulcerative Colitis. I immediatey told my boss (a Exec VP) and all was fine. In 2004, a fellow coworker J. started reporting to our boss (who travels a lot) that I was late everyday, taking long lunches, strolling around, not working, etc - which was NOT true. He believed her, not me. From then on, he began doing everything in his power to make me quit. He ignored me, chastised me for doing my job, reprimanded me on the false acusations, took away responsibilities and wrote me up in December for tardiness and absenteeism. Generally made it impossible for me to do my job at all - I was scared to leave my desk to go to the bathroom. I've been with them over 4 years and never had a negative review.
Secondly, when he wrote me up, ignoring my illness, he had never mentioned FMLA to me. So I went to HR and told them that he knew about my illness and that his actions were making it hard for me to do my job. They told me then about FMLA and I immediately applied and was approved.
Over the first 7 months of 2005, everything got worse with him and the stress was intolerable. It has caused a major flare up in my Ulcerative Colitis so that I've had to take off under FMLA and am scheduled for surgery. I've exhausted my sick and vacation so I'm into the last 4 weeks or so of unpaid leave. I have filed for STD. I also filed a complaint to our CEO just before this flare up about my boss's actions.
So - do I have any standing on any of this? I know it's not illegal for him to be a jerk - what about him not telling me about FMLA and then writing me up? What about the fact that the stress is a direct result of his treatment to me and is causing this physical illness? I've been reading on FMLA and I'm guessing that when I exhaust it (which I expect to) they'll just fire me to shut me up. Any info would be great. Thanks!