You must perform a hefsek taharah the day before you start counting, and the bedikot on the first and seventh day. We strongly suggest that you do one more bedikah on an intermediate day. That way, if you forget the seventh day bedikah, you won't have to start the count over from the beginning. (Should this happen, call our hotline for an immediate response.)
You may skip the moch dachuk until you are well.
Once given a clean bill of health, you should return to keeping all of the laws as you originally did.
You should see your physician for treatment of the infection, if you have not already done so.