if it was just polished which is what im thinking than the crank is fine. You can use oem bearings with an aftermarket crank. thats what sizing is for.

usually a knock under engine accel is a rod bearing. make sure you torqued the rods properly. how long have you let the engine run for? what is your piston wall clearance? if it has never heated up then maybe you should let the engine get to OT and see if it still persist, if you have a slightly larger than normal clearance on your walls then it can cause a slight "knock" until its heated up.