I am a codes inspector. First regarding the C.O. if one was never issued then you will want to let your local building official know so that from a code standpoint they can ensure that it meets all building code requirements. Typically, you will not be evicted just because a C.O. has not been issued unless there is a threat to life or health which from your message that may be the case. The codes department will issue a notice of violation for correction. Regardless of the lease provisions for who will conduct repairs typically the "owner" is held liable for repairs. Your local codes office can you give you some direction. I am not an attorney but from expericence in my field the judge will not side with you for not paying rent because of the homes conditions. Typically, a person would set up an an escrow account with the courts and escrow the rent until such items are fixed.