9.5 to 10.5K ohms is normal for a cap so that is good. Was the cap not seated on the plug or was the wire was loose in the cap?
I ask as one shows someone was there before and the other is a design flaw which allows the wire to get loose in the cap. Did you follow that link upstream
http://www.600riders.com/forum/fz6-technical/48874-cure-bad-vibrations-spark-plug-caps.html , that happened on my own bike and make s huge difference. I never lost a cylinder but had a vibration that wasn't there earlier.
Also I am not fan of the side strap grounded spark plugs NGK CR9EK and have installed CR9E's with the conventional single lug ground strap gapped at 0.0275" as the coils barely have the energy to jump the OEM gap let alone anything more. The side strap plugs are harder to gap accurately and wear faster than the conventional end gap plug.
In short;
- Make certain the gap does not exceed 0.028" .
- Make certain the wires screw into the caps and STOPS turning. If the cap spins freely on the wire, you have grounds for lost energy that is not delivered to the plugs spark gap.
- With 4 fresh plugs and the wires corrected, it shout be smooth. I have 100% visibility in my fairing mounted mirrors throughout all RPMs. The bike is smooth. Should it not be smooth, pull the suspect plug and replace it.
- Run it hard and NEVER lug it. Lugging an engine c0cks the piston in the bore and unseats the piston rings on some cases.
-Remove the synthetic oil, it won't break the glaze on a cylinder as quickly as a dino oil.
Note - plug changes are easier if you pull the two bolts form the radiator and it drops down a few inches making this task much easier.
I know my words seam like a huge stretch and would come off as a miracle but I've seen it happen way more times this this single case with your bike. It will take a 1000 miles to fully seat the ring and clear the carbon and sludge sticking them. THE ONLY WAY IT WILL BE SUCCESSFUL IS IF THE PLUG FIRES EVERY TIME. So if it sounds rough, replace the fouled plug.
You finding the cap loose matters as it all went down hill from there.