he was pettioned for a few years ago and we were just waiting for a decision
If he had a pending petition and he came here illegally, that was pretty foolish. As far as what can be done now, you'll need to speak with an immigration lawyer for an answer. More information is needed.
Hire an attorney. He may have just destroyed his ability to process under existing petition. A very thorough immigration history has to be analyzed. This is not the forum for such a complex issue. You need to sink money into this and hire someone.