alignment is defferint than journal bearings clearences although if the clearence between the shaft and journal bearings pads high it will create misalignment.
so during machine overhauling you have to check the journal bearing clearance while the equipment is de-couple and you have to be sure the bearing housing bolts are all tight. Thin you have to install dial gauge in the bearing housing thin let the tip of gauge to touch the surface of shaft and make it zero thin left the shaft by chain block must not exeeding the range been offerd and recommanded by vendor or manufacture.