I followed a similar problem for some time. Therefore I've started some investigations and created an experimental frontend.
The intension was similar. Let the user choose from a subet of X items and create one new part out of it.
https://stlcreator.mac-au.eu/indexb.html
There's a php engine in the background which generates a new stl where all the parts were connected via a sprue.
The system can be configured to deal with new items of my production.
Unfortunately the upload interface stopped working after the first trials and I never got it running again.
(currently it fails with another failure maybe the interface has been changed)
[Correction: I get a Mail that i have uploaded a stl fiile but the model doesn't become visible in the my models page
that could also be caused by a failure on my side. If I upload the stl file per hand it's normally ok]
To be honest I think this topic is very difficult to solve on the shop owner side. There's a request in the shapeways' feedback platform to deal with this topic but so far the effort seems to high ...
Woody64