1) use PVC pipe, if you are going to do this like this don't skimp on the forming materials, it should also be easier to get the correct form with the PVC
2) for the height, mix up a certain amount per tube, then pour in the same amount per tube, that coupled with setting the head on a perfectly level surface should help
edit: once you get it set and remove the PVC, you should be able to check the height of the bungs via a level, straight edge, and feeler guage... should work quite well once you get everything setup correctly
i wonder if you should groove the head where the JB will sit to help it have something to adhere to other than a flat bare surface