Are you having a parallelism issue with the spindle too? At any rate I use this tool quite a bit for troubleshooting the type of issue that you are referring to. Just mount it and use it along with an indicator and/or a Haimer.
MAGNETIC CYLINDER SQUARES by Suburban Tool, Inc.
It really helps when setting up to perform bore operations. You can indicate vertically or mount it to the table horizontally and indicate along its length. Look around at the usual tool disposal sites and I am sure that you can find one. I keep mine stored away with my master set of gauge pins.