Sorry to be so late with an answer to the toothpick ideas. Just got back from a week and half visiting the Oregon Coast.
I don't remember who I got the info but I have found it works. I make sure the toothpick is the same size as the hole, with not to much space around it. The reason for that is you are going to glue the toothpick into the hole. Push it thru so it sticks out both sides. Of course you are using round toothpicks. After the glue sets, cut off the toothpick with a dike just a touch from the wood. Then sand it smooth to the face, on the bottom. The top can stick out a little. The glue on the toothpick holds the wood together all the way thru the stack.
My junk layer is on the top. I don't worry about fuzzies on the bottom, and I don't worry about the pattern sticking to the face of the stack or whatever I am l cutting. Intarsia I don't worry bout the pattern sticking for obvious reasons.
I do like this system and for me, it works.