"In any case, I feel that I am being harrassed and would like to know if there is anything I can do?"
I don't believe it is harassment. Let me give you a different perspective.
"I informed the Senior VP that I was leaving early due to FMLA ...Right before I left, my doctor returned my call on my cell phone."
You informed them you needed to leave early due to being ill and then the CEO sees you in the break room talking on your cell phone. He/she has no way of knowing you are talking to your physician. For all they know you are making weekend plans. Generally when an employee is leaving sick they just leave they aren't in the break room or anywhere else on a personal call. And yes, even if you are talking to your doctor it is a personal call.
When you have to leave on FMLA just leave. DO NOT delay and do anything that gives the appearance that your departure is anything other than above board.
"Today my boss called me into her office to say that she was taken aback that I took an FMLA day on Friday and Monday, with Easter being on Sunday."
The problem is your timing is that you needed the time last minute around one of the seven holidays that employers recognize. It seems suspicious that you ONLY need FMLA on Fridays and Mondays thus leading to three or four day weekends. The employers I have worked for have all had a policy that if you call out sick before or after a recognized holiday you are not paid for the holiday in order to keep employees from abusing the time off and having mass "sick outs" in order to get more time off.
I think the issue is that you are stating your illness ONLY flares on Friday or Monday leading to long weekends. Even though you haven't abused it, the timing of the absences is what is getting attention not your illness or that you use FMLA.
I would suggest that if your physician is not finding a cause or a way to treat this that it may be time to consult a hematologist and get to the root of it. I would also be looking at the timing of absences and consider that perspective when your employer reacts the way they do.
"That's just my opinion, then again I might be wrong." Dennis Miller