1994 Honda Civic Odd Shake and Shimmy with the engine

Ok I will try to give you as much detail as possible.
Three Weeks ago my water pump broke, so I had a mechanic replace the waterpump and timing belt. It has been running fine since. My wife took it to work one day, and parked it. That afternoon she got in and started it and that is when the problem started. At idle it ranges from 600 rpm to 1100rpm. When you give it some gas with it sitting still it pulsate through the rpm range but it is worse between 1500-300rpm. I have ensured that I have spark to eat cylinder, and I did a compression test and found all four cylinders @ 190psi. I then pulled one plug at a time while the vehicle is running and only on cylinder 3 when I pull the plug while the vehicle is at idle, it doesn't change how the engine idles whereas the others make the engine want to stall since one less cylinder is firing. So I thought it was an injector, so I switch cylinders3 injector with cylinder 4 injector, but to my dismay Cylinder 3 still has a miss. I wiggled wires while the vehicle is running to see if there is a broken wiring going to injector 3 but nothing change. So the next morning I went to check it out again, I started the engine, and started pulling spark plug wires, and shocking cylinder 3 was firing however the car was heating up, than a few minutes later after the car warmed up and it idled down I pull spark plug wire cylinder 3 again, and it doesn't change the engine.
So my question.
Since this started all of the sudden and because I recently has my timing belt changed, could the belt jumped a tooth on the cam which would cause it. I am wondering if the valve is slightly open on the exhaust when cylinder 3 fires thus releasing the compression and thus no change to the idle when I pull a plug wire.