Unlikely that an ignition problem would result in a knock "unless" there was play in the wrist pin or rod to c/shaft areas. That can be checked as follows:
(Piston Play Check)
(J. Reeves)
This procedure will tell you if there is any wear or play in the Wrist Pin, Wrist Pin Bearing, or Connecting Rod to Crankshaft area.
Remove the spark plugs. Insert a screwdriver, dowel, punch, or some object of your choice through the s/plug hole and into the cylinder/piston area. Hold the tool lightly against the top of the piston. Turn the flywheel by hand, bringing the piston up to top dead center, then continue turning the flywheel to pull the piston down about a inch..... all the while holding the tool lightly against the piston top.
Now, at the point whereas the piston has been dropped down about a inch, grab the flywheel and hold it firmly. Now, push that tool solidly and firmly against the piston top.
If the piston moves without moving the flywheel, there is a problem (wear, play, clearance, etc) somewhere with the items mention in the first sentence. Be sure to check all of the pistons/cylinders.
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You describe the problem as a "knock" above idle. How far above idle... the higher rpm range?
Could this knock perhaps be a sensation that the engine is hitting a submerged object time and time again, resulting in a jumping action at the transom?