Another issue with the company my wife has been working for is that they state that any vacation time that is not used during the year will be forfited and you have to request payment (its not implied).

My question, she has been working here for about 3 years now, and we just found this out. Can she get paid for the unused days she didn't use in the last 3 years, or is it too late? Is there a california code that states this somewhere?

No, it is not too late. She will have to file a claim with the Division of Labor Standards Enforcement. In California, once vacation is earned, it cannot be lost.
http://www.dir.ca.gov/dlse/FAQ_Vacation.htm