Had a new water pump and timing belt installed, now car has a miss when idling?

What is your question?

My car ran great before the water pump & timing belt was installed. It still runs good, but when you first start it, it feels like it's running rough, and the car shakes a little sometimes, but you can't feel the miss when your driving on the freeway. Can someone please tell me what the problem might be? My son thinks it might be the vacuum line? Will I have to have the water pump and timing belt taken back off to find what the problem is? I'd appreciate any advise from someone who knows about the Infiniti QX4, thanks!