Мой дом наводнили крысы.

Quote Originally Posted by dinlot View Post
крысаы - (I am not sure of this; this might be irregular but it is animate accusative plural according to the table)
вода - воды, зима - зимы, труба - трубы, крыса - крысы...

It is not accusative. Крысы is the subject (nominative) and мой дом is the object (accusative).
Compare:
Мой дом наводнили крысы. - Literally: Rats flooded my house. Rats is the subject.
Мой дом был наводнён крысами. - Literally: My house was flooded with rats. My house is the subject.

Quote Originally Posted by dinlot View Post
наводнял - imperfective past; infested with rats in the past and still infested to present.
It should be in plural, since the subject крысы is in plural. наводнял -> наводняли

Also, the aspects work another way in Russian.

Imperfective is a process, a state, or an iterative action.
Perfective is a completed single action or a completed transition to a new state. No matter if the state is retained or not. So:

Present Imperfective:
Мой дом наводняют крысы. - the state in present: rats ARE flooding.

Past Imperfective:
Мой дом наводняли крысы. - the state in past: rats WERE flooding (at some point in the past) or rats flooded (many times, iteratively).

Past Perfective:
Мой дом наводнили крысы. - the completed action, resulting in a new state: there were no rats and then they appeared, so "flood" is "logically completed".

In your sentence, Present Imperfective or Past Perfective can be used.
Past Imperfective sounds here like "My house was being flooded with rats, when..."