[James]

While the crank is out you should check the connecting rod for out of round. While it was knocking it might have cause the rod to go egg shape. To check for it place the rod cap back on the rod and torque the nuts then mic the rod end, it should be round. If not corrected it can cause your rod to knock again and you will be back to square one again. If you're not able to check this the machine shop can do it for you. If it is out of round they can resize it.