I am an American citizen in love with a married man. He is from South American and entered into a marriage about 2 years ago. But after a year, the marriage fell apart. They have been separated ever since.

He has received a conditional green card based on his marriage.

During their separation, his wife has fallen in love with someone else (also a US citizen) and would like to speed up the divorce. Since they are both on good terms, the wife will wait to divorce him so that his permanent residence is not jeopordized. She has a agreed to file the petition with him to remove the conditional status.

How long after he receives the permanent residence status can he divorce her and marry me? I'm not looking to get married within in a year but perhaps even 2-3 years. How long does his wife have to wait to remarry as well? She would like to marry right away.

I would think as soon as he gets his card he can divorce and remarry. I don't see where it would be a problem but I'm not sure.
You may want to call a lawyer to double check but that's why there is the conditional period to make sure that the marriage is legit.

The thing is that they will ask for proof of continual marriage when he applies for his conditions to be removed, like leases or mortgages in both names, car loans....if they don't live together, this may be a problem.

You may want to call a lawyer and ask him/her about the conditional status being removed.