Hi,

This is just an off hand thought but it sounds like thermal expansion could be the knock. The exhaust system come to my mind. I know after a shut down you will hear the pipes cooling down. That's mostly heat shields.
If they get loose they can buzz at certain RPM. You may also check the bracket down near the transmission that hold the exhaust pipes. It can crack or lose it bolts.

Since this engine was replaced, that in its self, could warrant an inspection underneath.
Since you are having hesitation under acceleration there may be a blockage or restriction in the exhaust flow.
First thing that comes to mind would be a catalytic converter that has collapsed internally. Sometimes the chunks of honeycombs can travel into the mufflers. Mufflers can collapse from rust too.

I sincerely doubt an electrical relay can cause any knocking but they do click! (:-) Now a great big 100 ampere, three phase electrical contactor clunks.

Phil