Nick,
Maybe you could use slo mo video to figure out what's causing the knocking. Could be some wear/slop in the holes in the con rods that ride on the crankshaft--they tend to get oval-shaped over time. Another place to look is wear in the con rods where they join the piston rods. In either case the best fix would be to make new rods, although reaming and bushing them might also be possible. If there's this kind of wear you should be able to see and feel it.
Brent