Have you tried inspecting / replacing the ignition coils? Could be a crack in one of them that's causing spark to ground out before it gets to your wires.
Other fun diagnostics - check for proper compression on all cylinders (0 compression on any cylinder would cause symptoms that are far worse than you've described, but marginal compression will certainly contribute to a misfire), examine the exhaust for steam or monitor coolant levels closely to make sure your engine isn't sucking coolant through a blown gasket (water in the cylinder... uh, yeah that'd be bad).
I wouldn't worry about the plug seals leaking. Water may get down to the top of the plug, but the threads holding the plug to the engine will do a good job of keeping it out of the cylinders.