Alright so I was infected with the vampire disease, so I went to the chapel and got it healed. Now I barely missed curing it by like an hour but I noticed when I cured it my athletics was lowered to one from thirty. How can I fix this?

Try this in the console;

sdt 8
tdt

This will list all current magic effects on the player. See if anything appears there... In the mean time try;

player.setAv athletics 30