Did this happen the EXACT moment the exhaust was put on?
Have you checked the basics? Carb clean, timing set, no plug wires arcing, etc.?
Changing the exhaust should have no affect on an engine idling. May pop and make different noises. But not enough to change how it actually idles.
Now to clarify another item, will idle fine on it's own? Or is this just an issue when lifting off the throttle? RPMs drop low, wants to die, but if stays running will idle fine? Trying to determine if this is an idle issue or a transitional issue.