Did I ruin my chances for grad school?

Well, a 3.25 isn't awful as most of the people that go to College/University and don't put a lot of effort into studying but don't party a lot have 3.0-3.1according to a recent survey I saw, unsure who conducted the study so don't know how creditable it is. You could retake the calculus and organic chemistry and see if they will erase the previous grades or explain what you went through and get proper medical documentation and ask if there is any way they can let you retake the class and if you pass they drop your previous grades and give you the new ones, same with the thing for your gen. chem. and physics. As long as you do well on the GRE then you should be able to place in some of the mid to top tier two grad schools. My best friend's church friend went to college and graduated with a 2.95 Cumulative GPA and place into one of the top 175 best education>counseling and guidance education grad schools in the country. If they ask about your GPA be completely honest and say that it is no excuse but you gave school your best effort while you were sick.