Cleaning the mud or wasp-nest out of those drain holes and blow-drying the sparkplug wells (with the plugs in, of course) is a must for ALL CX/GL owners at least annually.
Before you even think of removing a spark-plug at ANY time, you should blow the well clean with compressed air.
If you go to a bike shop, and the mechanic doesn't blow the spark-plug well clean with compressed air before he removes a plug, then find another bike shop and mechanic for your succeeding maintenance visits - the first guy is NOT worth paying, as he doesn't take enough care.
I had the exact same thing happen to me last summer. First I thought it was the spark plugs, as it seemed only one of my two cylendars was firing, then I thought it was the oil or the fuel (flushed the gas system, cleaned it out with sea foam, oil changed) still only getting half power. Finally I pulled out the air filter and noticed it was quite dirty, so I pulled it out and tried running for a bit without it. Almost instantly I was firing properly again. Remember, that gas is not the most important fuel used in an engine, AIR is. So I have a good feeling that replacing or cleaning your air filter should do the trick.