Hi Dafydd - we would be happy to work with you; we're a certified partner & expert of Shopify that has used the API to do exactly what you are asking for. We have done this for various clients wanting to offer kits or bundles as a product choice - but have the product counts removed from other single item inventory.
Please contact us at projects@whitewatersolutions.com to discuss further.
Happy New Year!
WhiteWater Web