Edit: I just realized I was making this way harder than it had to be. See bottom, but keep reading my rant if you wish.
Here's a rough GIMP diagram of the alignment jig I proposed above:
Basically you would pull on each string and hold it in place with some sticky tack, going from string to string until you get it exactly level. Well, it doesn't have to be EXACTLY level with the waterline (or epoxyline that is) but it should be pretty easy to get it damn close. You can use the existing plastic flash of the original connector as a guideline. And since the resin will be water thin until you add the hardener, you can take all the time you need.
If you wanted to use that method, you'd probably want to build a little setup onto a peice of plywood or something first. If you're like me and you have a ton of scrap metal, wood, pipes, electronics, plumbing stuff, anything you can imagine lying around your house that your dad has been saving for the past 40 years, you should have no trouble finding something to work as those bar thingies the strings attach to. Especially working on such a small scale makes it easier.
However it would probably be more simple to settle with an uneven mold, which would only work on plugs that don't have any curves or specific points where they become symmetric, otherwise it would get totally messed up. You could do like so:
The purpose of the nail polish is to make sure the plug sticks to the bottom mold and makes a nice seal so the new epoxy won't flood under the plug and wash it away. Nail polish remover is easily removed by just snapping the plug out and cleaning up any excess with acetone (which damages plastics, including epoxy and the plug no doubt, so be careful. It won't melt it, not very fast, but be careful) or even better, a plastics safe electronics contact cleaner (any electronics contact cleaner for PCBs and stuff is plastic safe). Then when you're finished you have two half molds, and if you casted them in the same size container (like above when I said a square container and another, same size square container which is taller) you'll have a perfect, square fit between halves.
I'm probably still not clear, but I'm going to try this in the next few weeks, and if it works like I think it will, I'll write a tutorial and make a simple video showing the technique (probably using SketchUp since it has simple tools for that).
Edit: I just noticed that in my last drawing, it shows such a huge margin of error that the pins are completely encased in epoxy. That would be bad. As I said, the uneven method doesn't work for round objects, which would include the pins. However if your margin of error was low enough it should work. Although you still may want to think about that centering rig or even something simpler. Simple...hahah, I just got it.
Sooo simple. You'll want something flat, like a peice a sheet metal, some high quality wood, or best, a peice of float glass (which will be almost perfectly flat, well beyond what we would need, but still the best). Using some light adhesive such as nail polish, or, if you are trying to adhere to glass or plastic and roughening the surface doesn't help, you can use a small dab of silicone adhesive sealant, which you can buy at any hardware store. Use a VERY little bit, just enough to make it stick, and you want it to be as FLAT against the wood/metal/glass/etc as possible. Then it's simple. You get any containter with a flat top, like a film container (the little cylinders). The shorter the better, because you don't want to waste epoxy. And because it's easier to clamp later. I can't think of anything specific that is that damn tiny, but you can probably find something somewhere. The lower half of an Altoids container, perhaps. The flatter the rim the better. Then just drop the flat metal/plastic/glass/etc with the plug glued onto it on top of the container, and pour in the epoxy resin and add the hardener. Well, okay you'll probably want a hole in your flat surface to make that easier. But you pour it on (with the container on a FLAT surface like a good kitchen counter) veeery slowly until the waterlevel reaches your exact halfway point. Do that twice for two molds, or continue using the make-the-other-half-by-molding-it-against-the-first-mold-with-the-plug-glued-in-place method I mentioned above (the diagram with the nail polish stuff).
Wow...that probably made no sense. Again. But as said, I'll come up with a good video showing the technique after I master it. If it all works out as it does in my head, the entire build time for a custom plug should be a matter hours including epoxy hardening time. Materials cost will be somewhere around 10 or 20 dollars, the closest hobby store to me sells like 10 or 15 dollar jugs of epoxy casting resin and hardener for a few bucks. But it's good stuff to have around anyway.