FMLA/Stroke/termination

I had a mini stroke on Oct. 3, 01. I informed my employer and my doctor wrote a note explaining that I would be out of work for an undetermined amount of time. He wasn't sure what was wrong with me. He suspected a stroke because of my symptoms but had me take several tests and even talk with a psycoligist. In Feb. he finally determined that I did have a stroke and started my Physical Therepy. The stroke was stress related from my job. I know this but at the time I didn't explain this to my Doctor. I couldn't speak very well and had no real memory and couldn't even write my name with out problems. My employer put me on paid 6 month short term disability. My employer also started FMLA. I didn't request it, sign anything and didn't even know it was being run concurrent with my short term. My questions:
Can they run FMLA without my knowledge?
Is it the law that they would have to run FMLA again in the new year 2001?
Can they terminate me as soon as my short term ran out without any prior communication about termination. I might have been able to return to work in May but wasn't sure until I saw my doctor. They sent me a termination letter on April 6, was terminated on April 1, and Short term ran out on March 31, 01. Please help!