Since you obviously know about the lead it will not be an issue. As long as your wife isn't literally chewing on the house and consuming the house you should be OK.
Nothing you mentioned needs permits, so the city doesn't certify anything. Frame work only requires a permit if the footprint of the house itself is being altered, either gaining or losing square footage. Windows never do.
As far as the late fees, no that would not be a lease violation, but illegal fees do not have to be paid. I can't think of a single state that does not allow them though.
Alright, there's a couple of issues:
1. If they are not compliant with local codes, you ask them in writing to fix the situation. If they don't, then you call codes and codes will either compel them to fix it or condemn the rental.
2. It is best to just air your concerns with the LL first. He'll probably want you gone rather than deal with the hassles and let you go it peace.
3. I am of the same mind as acermill. So many times tenants rent a place, have a change of heart, and then go looking for material defects as an excuse to break the lease. I do not know the condition of your apartment. If its bad enough, you have a right to go. But, courts are also hip to the tenant trying to fink out of a lease. That's why you need to go through codes first. If codes says its violating code, you have a case. If not, you don't.
Were I your landlord, I'd allow you to leave without penalty. Why? Because you sound like a problem tenant. You're whining about several issues only a few months into a lease. Landlords really do not need or want tenants like that.
Speak with the LL and tell them they can let you out or you will call everyone you need to in order to get them hammered with fines. etc. You won't have an issue.
In the future, assume any home built prior to 1980 has lead paint in it somewhere.
visit your state's government for info.
