... because I have been using gray RTV sealant on the side cover ...
Gray RTV? Are you sure you aren't using Yamabond or Hondabond? These are actually butyl rubber and not Silicone. Those are what I use to replace any gasket that doesn't require a "special" gasket. Wipe a little on both surfaces, then assemble a few minutes later and be done. It to can get into passages but you have a little more control on its application.
Do not let this send you on a wild goose chase, but....
If your tap is still there after all of this, I have something you could look at that SISF wants me to look at on my motor after a conversation with him. I got a motor of unknown origin to replace the one that blew back in June from a bad crank bearing #3. The valves are set correct, and I have since added a manual CCT. I still have a tap that is coming from the top end, seemingly near piston 1. Short of piston slap or a wrist pin being bad (and I think the sound would come from a lower point and would go bad fast), mine is perhaps a rocker arm that is worn on the pad that rides on the cam lobe. The only way to check this is to pull the camshafts out. Next time I open it will be to inspect the lobes as it might tell we which one it is (if this is the problem). Otherwise it is a new engine for me. Right now it is just an "around town" bike and the sound hasn't changed, so i'm just waiting for the cold weather to give me a reason. At a minimum, since the valve cover is already off, get a bright light and a magnifying glass to inspect the lobes close up.
Hopefully it is just your valves. You never need to take the ign cover off if you do the starter bump method. It is extremely simple.