[mlabruyere]

A bubble level will NEVER give you the angular resolution you need to get your Z-axis perpendicular enough.
You need a 12 X 12 sheet of glass, a deck of cards and a dial indicator with a beam-mount.

1) Lay the sheet of glass in the middle of your work-bed and mount your dial indicator into the router chuck, so that you have at least 3 inches of radius of rotation.
UNPLUG YOUR ROUTER!
2) Rotate the router by hand until the indicator is aligned along the X-axis, then move your entire gantry along the same axis as you "read" the surface of the glass. Do not rotate the indicator at all, this is a straight-line sweep.
3) Add shims under the glass until your indicator stays at ZERO from the front to the back of the glass sheet.
4) Rotate the router by hand to align the indicator on the Y-axis, then swep along THAT axis to read the surface. Do not rotate the indicator at all, this is another straight-line sweep.
5) Add shims under the glass until your indicator stays at ZERO from the left to the right of the glass sheet.
Your glass sheet is now parallel to your ACTUAL X-Y plane!

6) NOW, slowly rotate the router (sweep it in the 3 inches of rotational radius) and read the dial indicator. Adjust your router head by whatever means your machine has available until an entire rotation of the indicator produces less than 0.001" of deflection.
Your router head is NOW perpendicular to your true X-Y plane within 0.001"!

You may need to resurface your spoil board when you've completed this, especially if it took more than ONE playing card to level that piece of glass. One angular degree equals 0.017 per inch per degree, so if you needed 2 cards (approx. 0.019") in 12 inches, your bed-surface is approx. 1/12 of a degree (6 arc-minutes) out of square.

Thanks Dorsal! I'm going to give this a go....after I locate a dial on a beam mount.....