I thought about that also Chopper. I'm thinking though if I can go in a downwards motions instead of going side to side, it may help that some. Will definitely take alot longer, but atleast I wouldn't be working it into the crack between the wood and plexi. I also have the big silver knob for it so it will cover it up quite well.
McHale, Stepper bit would work great, and I know they work much better on plexi than other bits, but if that thing somehow grabbed the plexi or wood and my plexi got cracked I would be heartbroken. I think I'll take the safe solution and just use some sandpaper. Shouldn't take much at all with some medium grit paper and a little elbow grease. I imagine the hardest part will be keeping the underside of the plexi clean.