Hey Fatman - the easiest mold modifications are done with epoxy putty. (There are multiple brands to choose from, but I go with JB).
Just pinch a little off, mash it around to mix, put it in the mold (with the hook, keeper or whatever you want in position) and close the mold to form; then use wire or small nail to remove the portion you don't want filled in, and let the rest harden.
The putty stays put when tinkering, and most have at least a five minute working window, so there is plenty of time to get things just how you want them. I've used putty to modify my panfish jigs to accept smaller hooks and it's pretty much a cinch... I wouldn't let it scare me if I was looking to modify as you seem to want.