Mysterious cold/flu after 2 weeks...what can it be?

Ok...This might get a little long...

First off, my g/f is on the pill. She tried it for the first few months. (If you guys need the specific kind of pill I can get it) After month 3-4 she started bleeding on a regular basis. So, we decided so switch to different pills. We went to the doctor for a different brand and he said no sex for 1 month. She just got what I thought was her period but I'm not so sure. How long and short can periods be? This "Period" was only 3-4 days. Is that too short?

I figured it was her period so when she was done we had sex. Without a condom. Before she got her period she had a very bad cold/flu. Sore throat, heavy coughs, headache, stomachaches, the works. Problem is, she's still sick to this day. Are some side effects of b/c pills reduced immune system? Or can they make the user sick all the time?

I'm so worried that she might be pregnant. We've only done it 3 times since her period. And I've pulled out everytime ( If that makes a difference)

What are the chances of her being pregnant? High, Low?
Is the mysteriously long cold a symptom of something?
How short can some periods be?

I need all the help I can get. I'm worried sick.