From my own personal understanding and from the description, it doesn't sound like you have a very strong case. Simply because the upstairs tenant was unhealthy and (perhaps) a nuisance isn't very strong ground to countersue, especially since as soon as you signed the lease, your co-lessee had moved out, therefore voiding your agreement (unless your other roommate was subletting the lease from your ex, which from my understand through your description doesn't sound like the case). I'm not an expert or anything, but it doesn't sound like a strong case. Best of luck with the situation, though.