My honda civic stumbles at low rpm whats wrong?

changing the exhaust system can alter the gas flow and may create problems for the sensors . The HO2s sensor and the O2 sensor may now be operation on the edge of the parameter settings and any exhaust coating on the sensors may be affecting their performance. Run fault codes to check the sensors and sometimes removing them and cleaning them in vinegar to remove the coating will improve the situation. What ever is the problem if it started after the manifold change then that is the area in which to seek answers.

Incorrect spark plug gap sub grade fuel plugged fuel filter emissions faulty electrical problem need more information

Whats the rpm at? Could have a number of issues, Idling, timing belt, low coolant, low oil etc..

700 to 900 rpms after warm up

it sounds like you have a vacuum leak or the throttle plate needs to be cleaned

sounds like the motor mounts are bad,have them checked out.

It sounds like the A/C compressor may need to be replaced as it sounds like it is bogging down the engine more than it should. This is not so noticable at higher engine speeds.

fuel pump pressure too low.causing lean mixture .

either low coolant or your IAC motor is acting up

I assume you mean low idle speed 500 rpm. Genarally a tapping noise comes from the valve train, and a knocking noise comes from the crankshaft connecting rods. The way that a mechanic will narrow it down is to use a mechanics stethoscope. You can get one pretty cheaply at an auto parts store. Put the metal end of the scope on a part of the engine and listen for noise. On the other hand, if your car is idling at 5000 rpm, it would also be making ALOT of noise.