Here are some further alignment suggestions, with photographs uploaded to a new album.
First photo:
My Vertex 6" RT is fitted with an adaptor with a Myford spindle nose, which itself has been centred on the RT so that the spindle nose is accurately located relative to the RT's centre or rotation.
The RT is placed on the mill table, but not bolted down. With an accurate bar held in both chucks, the RT can then bolted to the mill table, centreing accuracy being dependant on the accuracy of the chucks, of course. WIth collet chucks, the accuracy should be very good.
Second photo:
Same idea, but this time to align a mandrel with the vertical spindle – grip the mandrel in the spindle collet chuck, then bolt the angle plate to the mill table. The component (in this case the regulator bush for my boiler) can then be drilled and tapped.
Third photo:
On the right is a 3MT blank end arbor with two diameters machined on it, 19 and 20mm, to fit the largest sizes of ER32 collets. The Omnimill vertial spindle is bored 3MT, so this fits directly in the vertical head. Why two diameters? Because the Great Law Giver Murphy has decreed that whenever alignment is required, one of those collets will already be in use elsewhere!
The various tapered mandrels are used position pre-drilled holes under the vertical spindle – mandrel in a collet chuck in the vertical spindle, poke the tapered bit into the hole in the workpiece, then clamp the work to the mill table.
The two methods work well in combination – use the 2-chuck method to centre the RT, remove the chuck from the RT, substitute the faceplate, then use a tapered mandrel to align the hole and its surrounding metalwork on the faceplate – clamp the work to the faceplate, and everything's set up for milling around the hole.