I have a '99 Audi A4 quattro. Its the avant (wagon), manual transmission and 1.8L engine. Recently the check engine light came on and began to flash. It was idling rough and driving rough until about 3500 rpms. I took it to autozone where they ran a diagnostic test. The code come up as a cylinder 3 misfire. I replaced the spark plugs, but the problem continued. I then removed the spark plug wires one by one, starting the engine after each removal. The car started after taking off each spark plug wire and ran equally "rough" each time.

Would removing the wires also be a method for checking the master coils? Or is it still a possibility that a master coil is bad and I should switch them and see if the misfire also moves with the master coil?

I haven't had time to return to autozone and check the code to see if its still cylinder 3 that has the misfire (its possible I didn't gauge the gap well on the spark plugs). Thanks for the assistance in advance.