1999 Lincoln Town Car Intake manifold was changed due to a

Engine Mechanical problem
1999 Lincoln Town Car 6 cyl Two Wheel Drive Automatic 250 K miles

Our Lincoln had a brand new engine put in it in 2006. It ran well, until the intake manifold developed a crack. It was parked right away, and not driven. We brought it to a mechanic here, which we trust. The manifold was replaced. Since then, the car runs rough! It did not run like that before it was changed. The mechanic looked at the car again, and said he is stumped. They said the injectors were ok, spark plugs changed, and even changed the coil. WHAT do you think is wrong? They are stumped, and I just want my car back. Running right. Any ideas?