Any ideas what this came from. Could it be related to the clutch installation? The CEL went on about 5 minutes after I got the car back from the shop.

P0411 - Secondary Air Injection System Incorrect Flow

I looked at other posts with this code and I'm reading that it could be due to the vacuum hoses or backwards white check valve. Would anything related to this need to be disconnected when pulling the transmission?

 

This has been covered several times... when you performed the clutch job chances are you removed the stock air box and in turn got the vacuum hoses mixed around. Check post # 9 in link This is the diagram for the hoses. Pay close attention to the "white check valve" it has to be pointing the right direction to not throw the code. #1 in the diagram is the check valve I mentioned before