I have a product line with a few dozen part numbers with common & unique tests based on product family and it sounds similar to your situation, although at a much smaller scale. I use a product from an NI Alliance Partner called dTRAK (http://g2tek.com/dcp/i/products-dtrak).
My first thought while reading your post was to ask how much experience you have, then I saw the "CLA" in your signature. It's worth giving them a call, anyway, as they've already done a lot of the heavy lifting. Good luck.