Do you have(or know someone who does) the nessecary mikes, inside and outside or snap gauges and outside mikes to measure the inside of the main caps torque down with both the bolts and then the studs? If so make those measurements, if they don't vary more than .0002 I would run it as long as the main bearing to crankshaft clearances are above .0030 If they vary more than .0003 I would ask the machine shop to redo the align hone with the studs like you paid them to do it the first time They can't fix it if you don't ask them or allow them to