So can you tell if it's in the cylinderhead or in the cylinder block? If you can't, take a piece of plastic water pipe or even a hammer handle and with one end to your ear, press one end against different parts of the engine. This will help isolate and amplify the noise.
If your engine has a single overhead cam, the valves may simply be too loose. With double overhead cams, valves tighten as they wear.
If it's in the cylinder block, it could be a galled piston from lack of lubrication caused by insufficient oil level, pump failure or oil film failure from overheating.
If it does it only when cold, then it sounds like piston slap. The piston is just a bit too small for the cylinder but after it warms up, it's ok. My KZ1000 acquired piston slap at 35,000 miles and ran fine till I swapped the engine at 105,000 miles.
Make sure the cam chain tensioner is working properly because a loose chain will flop around and make noise. The '81 KZ1100's had an excellent non-slip tensioner while the 1300's still had the failure prone piece of cr@p they designed in '79. Not sure what your bike has.
If your bike does have a balance shaft, some are chain driven (like the ZG1200) and the chain must be tightened periodically.
Does this have anything to do with your question about removing the cam chain that I answered earlier?