Did you mark the rods and caps when you removed them during teardown?
Did you have the rods resized?
If you didnt keep the rod caps with their original rods, then you should have all the rods resized so the bearing crush is correct and your clearences arent wrong. Bearings are not supposed to be "worn" in, if the clearences are too tight or too loose, you will have damage on startup.
Did you clean the crank after you got it back from the machine shop. Never trust that everything has been cleaned from the oil holes, some shops only blow the outside of the crank off, and leave shavings in the oil holes, expecting that the customer should know to clean the crank before installation.
Are you installing the rod/pistons in the right dirrection, they have markings to show which side should face the front of the motor.