Oil pump chain broke, now engine knocks.

Long story short, put a new top end on the motor along with new timing chain. Heat cycled it to break it in. First ride our (night ride in mud), after running about 2 hours, temp light comes on, let it cool off, crank it up, temp light comes on…before the fan even comes on. Take it back to camp, crank it, check for air bubbles, check for water flow, check everything, finally check and see water pump isnt turning. Open case, water pump/oil pump chain is broke. All this time running the engine to troubleshoot and it hasnt been pumping any oil.
I get her back home, put new chain on, and everything runs great…for 3 minutes then I start hearing a knock, now its permanent.
Crank the bike, all is quiet, 3 mins in, knock comes back.
What am I in for here?????