Make sure the rod caps are the correct ones for that rod. They MUST go with the one they came from, and MUST go in the same direction. Some have a small dot to line them up. As you tighten them, rock them slowly.
Obviously you know which way the piston must go in the cylinder. That is important! Swooping side towards the exhaust, short steep side to intake.
Then, if the rods have oiling holes, they face up.
If the crank has counterweights, the rods will only fit one way.
Flat side of the rod faces the center main bearing.