I need advice on Immigration and Customs at San Francisco International Airport?

I am traveling to the US from South Korea on DEC 30th with my wife. I am a US citizen and she is Philippine National who just obtained a CR1 Immigrant Visa. Our flight arrives at 8:05 am at SFO. I am wondering how much our personal exemption for customs will be and how long we should expect to wait to get through it all. We have roughly 3 hours until our connecting flight to Chicago. Also, if anyone knows which counters/directions I should go in the airport that would be nice.