Car runs rough at first startup?

Make sure the intake gasket sealed properly and that you tightened the intake manifold properly. If the intake gasket is leaking, that could be what is making the car run rough.

Depending upon how rough the car runs the non-sealing of the intake will generally cause an engine to surge a bit as well. I am wondering if you got the plug wires in correctly as in seated right, if you may have cracked a plug or put a plug wire on the wrong plug.