Yes. Any time you change a cap (on a rod or main) you need to re-bore the assembly. Otherwise the parts won't fit together correctly and can create drag or lock up due to the mismatch in the bores. If you replace the main caps and do not align bore it, the crank can get locked solid when you torque the main bearing caps. This is why you have to keep them in the exact same order/position and on the same orientation when putting your block back together.
Always match the anchor slot on the caps with the anchor slots on the main bearings. Same with the rods. Put the anchor slot of the cap on the same side as the anchor slot in the rod. This will ensure proper orientation for the caps.
