While pulling the case halves together, the tight fit of shaft to bearing, or bearing to case has side loaded the bearings.
In simple terms, one or more of the races of the bearings - either inner or outer has been pulled sideways so that the balls of the bearing are not centralised in the raceways- you may be able to see or measure with feeler gauges a difference in the gap between the crank lobes and the case interior.
The issue is cured by belting the stub ends of the crank with a SOFT FACED hammer, think brass, lead or dead blow nylon hammer, so as not to damage the threaded ends of the crank, until the bearings become centralised and the crank rotates freely with finger and thumb rotating the con rod.