Here's where my lack of experience really starts to show. I spent the better part of saturday trying to fine tune the router. I attached a dial indicator and ran the router along each axis with a carpenters square clamped to the bed. I found several major problems with the way the router was configured and solved them one by one but couldn't get everything to run true. I'd get it to run square in the X direction and it would be way off in the Y.
My first CNC router was a JGRO built entirely by hand. It did a lot but wasn't very accurate or durable. Its biggest job was cutting out parts for a Joe's 2006 replacement for itself. I've almost finished assembling the new machine. Here's a purdy picture.
This is my first CNC machine. Built on the JGRO design. Lots of information on cnczone.