VERY Custom Stores

I have hundreds of options in two different parts of the custom work we make, I'm wondering how to go about making a "build a bear" feature for my woodturning projects.


(The Long Version)
Okay, this might be a little weird situation. First off, I'm a custom woodworker, specifically a woodturner, and I have two purposes for running an online Square Store: Selling-off my template items, usually "pens", and 1000% custom orders... I know that doing the former is easy, the latter, on the other hand...


So, there are literally thousands of hardware kits out there, any of which is at my disposal. I order hardware supplies from Canada, USA and China, each one in as many as 7 different finishes, and many have ballpoint, rollerball, and fountain pen variants. I also have access to hundreds of different kinds of blanks (blank = the bit of wood, acrylic or other used to MAKE a custom pen). 


I understand the purpose of the "variants" when a t-shirt is concerned (here's a shirt in 3-4 colours, with 3-4 sizes), but my issue is we have hundreds of different kits (hardware end-bits and cores), hundreds of different blanks (the pretty wooden bit in the middle), to speak nothing of optional clips, ink colours, spare inks, labels, acrylic variations, etc... 


One option remains that I could have a section on my website gallery, as different from the store proper, where people could "add to cart" a finished unit that represented their hardware choice, a finished unit that represented their blank/barrel choice, etc... and when they hit "buy it now" something custom happens... but that all seems/feels very clumbsy to me.


I really don't want to screw with having to have a sit-down conversation with every customer who has a reasonably simple custom order request when we have all the parts in stock... but when we make sample/prototype items, it's easy enough to put THEM in the store, but they're usually one-offs. We could list them as examples and try to work on making EVERY variety, but good lord, that would be a LOT of items and that'd make inventory/stock control a nightmare.


It had occurred to me that I could implement a feature whereby an item reaches "zero" stock, someone can be placed on a waitlist, and we'd get an email announcing that... but short of desperately trying to keep all standard parts in stock... you might now see my conundrum.


For those who want an example of what we're working on, our facebook group page is:

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