When I made wooden baits, I would shape, add the bill, hook hangers and line tie, and then seal the wood, so I could float test it for my ballast testing. That way, I got an accurate reading of what my lure would actually be like in the water.
I would put on the trebles and all the split rings, float it in a bucket of water, add split shot or egg sinkers to the tines of the trebles until I got it to float or sink like I wanted, then drill ballast holes in the belly of the lure and epoxy in my ballast. I would bondo over the ballast holes and sand it smooth, and then paint and topcoat.
Remember to subtract anywhere from 1 to 3 grams of ballast to allow for your paint job and top coat, depending on the size of your lure.
If you are using D2T as a sealer, try adding a couple of drops of denatured alcohol to it AFTER it's completely mixed, to thin it a little so it penetrated more into the wood.