This is coming along real nice Scott. That tool is at carbatec for over $80 so you got a good deal.
I'm working on an ES-1gt and have found the same problems you have with an asymmetric headstock, bridge post holes leaning back and pickup routes not quite the right size for the tonerider pups I'm using. Some plugging and redrilling taking place to be followed by some sanding, sanding, sanding and more sanding. The zen comment makes a lot of sense. I see these slow jobs as a chance to listen to some tunes when I'm not distracted by the cricket.