Very sick while/after visiting Costa Rica?!?

[Sydney]

I just spent 3 weeks in Costa Rica in the rainforest on a mission trip. During the last week of my trip I suddenly felt weak, got the chills, and was really tired. My nose started running over the course of the week, and eventually my throat got scratchy. The last few days of the trip I started feeling terrible. I assumed I was feverish (I had the chills, body aches, headache, constantly hot and then cold) over this last week, my throat pain was/is horrible, and I had a horrible headache. I couldn't swallow anything without my throat hurting. When I got on the plane to come back to the U.S., my throat was in excruciating pain the entire way, I had a runny nose, headache, and the constant changes in air pressure made my ears feel like they were going to burst. The six hour flight almost brought tears to my eyes multiple times because of how sick I felt. When I finally made it through customs after being on the plane for so long, my became extremely light headed and started sweating even though it was freezing in the airport (the man in customs even asked me if I was feeling ok because I guess i looked so pale). I've since been home for two days and this morning was the first time I was able to fully "pop" my ears from flying and be able to hear. I'm still extremely exhausted, have the chills, a horrible sore throat, etc. I was just wondering if this is just something that will clear itself up, or if I contracted something horrible while in Costa Rica?