We spoke over the phone... the issue was just understanding the "Track Separately" checkbox when adding options. Checking that box allows you to change price and weight and separately tracks inventory for those options.
That checkbox should only be used if the selected options effects the price, weight, or is tracked as a separate SKU with inventory control. Using track separately for a lot of options for a single product can dramatically effect page performance.
Once we checked that box while adding the necessary options it became clear how the rest of it worked.