How can I handle restricted items on a Drupal Commerce site with special display and checkout rules?
So found that I was mostly in uncharted water on this but I waded through and I am mostly done building, so I will explain how I did it for the next guy.

I used quite a few modules, including a few custom modules...

Commerce wishlist was used as a template to create two custom modules 'request a quote' and 'request a sample'.` They are essentially extra carts with custom actions.

Another custom modules was used to alter/disable parts of the commerce line item based on CCK field values. It will also be responsible for altering the checkout process/adding safety coniditions when I get around to that.

Taxonomy maintains a multi-dimensional product hierarchy. Tokens, Url Aliases and Views with 'global exposed filter' + views_php create the catalog. Views are embedded into tpl files and passed arguments programmatically from node properties in lue of using product references (I needed more customization/arguments) than they offered.

The answer in short to building most of my problems was to be very Drupal-y about it and ignore a lot of the out of the box functionality of commerce...Aka: Take the views hammer to it!

That's about it. Good luck future Drupal Commerce dev!