dublenaught,
Sorry to hear about your problem. Were the rods and mains mic'd by a machinist, deemed OK, and the appropriate inserts installed..how 'professional' was the rebuild?
From my experience, a rod bearing usually knocks when NOT under acceleration as the forces created will load the clearances up and negate the problem. If you rev the engine at a standstill, a rod will usually rattle as throttle is let loose and the engine coasts to a idle.
A main bearing usually will make noise under load, but it is a deep, hollow thumping. A broken piston can mimic a rod bearing but will be more tinny sounding.
Your idea of pulling a plug wire to ID the offending cylinder should have produced some type of difference if it were a rod bearing.
If your crank wasn't ground and matching inserts supplied, it's sort of a crap-shoot. The lock washer episode on the rod cap bolt doesn't sound encouraging either. Maybe someone will be along to give you a better answer. Good luck.
Stuart