Sounds like your changed out engines, right? If so, then you need to first look for the obvious things. Rough idle can be a number of things, but I would first check all your vacuum lines. A vacuum leak can cause a rought idle.
In the fuel circuit, you may also want to do functional test on your cold start valve. If the valve is leaking through, you could be running a rich mixture at idle........which could account for the stumble (and would also be reflected in poor fuel consumption).
Depending on age of the car, you may want to also proactively replace some ignition components such as your ignition wiring, including the distributor rotor and cap.
Those are a few things that can be done cost effectively and should help your situation.