My Callies crank measures between 2.7491" and 2.7494" on the mains and 2.1993" and 2.1994" on the rods. Doesn't seem like 0.0007" or 0.0008" under the nominal would be out of line?? I wouldn't expect the journals to measure right on the nominal dimension.
You might have to use half of an 0.001" under or 0.001" over bearing to get the clearances where you need them. I can't remember the last time I built a motor only using one set of bearings. I have a shelf of left over half shells...