Pull the starter out and see if u are able to pull the gear out on your own. If you can that gear can stay out slightly and hit the flywheel as mine did and needs to be replaced. I replaced the starter and had no more knock. Hope this helps.

 

I have a 2000 Honda accord ex with a 3.0 VTEC, I was going faster than I should and it was fine at first but the about 10 minutes later it started knocing real bad and I parked it as soon as it started for about a week and we just replaced one of the rod bearings and started it and it knocked for a second and then quit. Then we started it again and the knocking came back.

 

It sounds like it is time for you to find a new(er) motor from a bone yard and put it in; either that or do a full rebuild of your motor.