The limber holes themselves are more problematic. On his Grouper, Rick Nelson ended up just painting them on - but I like to see real holes in there. A perforated resin replacement slab is what obviously first came to mind. But then again, as you say there's the wide variation in hole-patterns between (practically) each and every boat - so a single replacement pattern, only applicable to one or two, would hardly be cost-effective to develop.
Where my thinking (I'm not going to say product development, as I'm so far behind on so many others) currently leans is toward finding the elements most common to all the hole-patterns, so that a "generic foundation" of holes might be provided, which would cut down to a minimum the remaining work the builder would have to do, to finish out the precise pattern for his subject. This is first of all a huge research project (already well underway), and then a mastering challenge (at least, done the way I would want to) of some complexity.
That's the best I've been able to come up with, so far...