What I would do in a case like this is to first, try to make all of the pockets the same depth. Then, cut some 1" wide strips of wood, of the appropriate thickness and the length of the shorter dimension of the pocket, to get the total thickness in the mounting areas to over .5". Round two of the corners, if it helps to fit your pocket profile better. Apply a liberal amount of wood glue to the strip, and lay it in the pocket. Clamp, or apply weights until it dries completely. Then, you will be able to drill holes for the threaded inserts and mount your sticks.
Not the prettiest way to do things, but if you do it right, it will save the panel and you won't need to drill new holes for the shafts. From the top, no-one will ever know.