John's method is a correct way of doing it if your opening up a small diameter bell for the larger retainer.The retainer will indicate the trans to crank centerline.Usually the when correcting the excessive run out you will find the 4 trans attaching bolts already have enough slop to allow the trans retainer to conform to the bell bore.It your using the correct bell/retainer then you need to adjust with offset dowels.The bolts don't indicate(align) the trans,the center bore does.