i do have a similar case for web-to-print products where the customer can freely choose the imprint, print technology, accessories etc... and build a 'dynamic bundle' . My solution is to use an external 'bundle configurator' and then send the selected products into the shopping cart through a web-service I have developed. In the web-service, programmatically I add a product bundle to the cart and then, also by programm, add all the selected products to the bundle.
This means that in the broadleaf admin, I have only one 'bundle' product which contains no products and one 'real' product for each ordarable product item.
These creates an enourmous flexibility on how to compose the bundles and also having more than one of such bundles in the cart.
If these is a path you might consider, let me know.