Andrew, I hate to throw cold water on your idea but I think, while the electronics might be quite easy to do, you could be defeated by the precision mechanics of the xy table. Such a thing is rather difficult to home built if you want a repeatable accuracy of 2.54 mm. Unless you use quality components (not cheap) for the mechanics and have the equipment and skill to work or modify them, it's going to be disappointing.
Much better to aquire a ready made xy table, one with toothed belt drive for fast response times, and try to get a program to work it. Even so, you need some kind of tacho feedback so the computer driving this thing knows at any time just exactly where the table is.
With regard to routing the tracks, a good Dremel motor might work but the price of the tungsten or diamond tipped tool bits will hurt the budget.
Which got me thinking why you want to do such a project? Just for a few home brew boards its way overkill. If you are planning to start up some commercial venture you might find it cheaper in the long run to get something ready made rather than trying to re-invent the wheel, so to speak :wink: