If the head is not Sq. to the table then it is impossible to produce good parts. your sides of the parts wouldn't even be sq. to your part. As you found out holes etc. will be off location also. On a bridgeport, for instance, the head has to be squared up all the time in order to produce quality parts and "Tramming in the head" is the first step in setting it up. This is usually only a problem on the X axis. Once the Y axis is trammed in it usually remains intact on any mill or Router.