The purpose of the fuel filter is to prevent any foreign debris that makes its way into the fuel tank from clogging the injector nozzles. So it stands to reason that some of the cleaning paper could be in the fuel filter, but a clogged fuel filter usually shows up as a flow restriction at higher rpm.
Running intermittantly on one cylinder suggests a plugged injector or an ignition problem associated one or both spark plugs. Pull the plugs to see if only one cylinder is affected, and if so, try switching ignition wires, ignitors, injector relays etc. between cylinders to isolate the problem.
One concern when servicing the fuel system is you need to be very careful not to dislodge any fuel line particles downstream of the fuel filter - they'll plug the injectors.