Just as a second thought, you could always diamond the smaller locating pins on your fixture, they don't even have to be diamond shaped, you can just mill flats on two sides so the pin only locates in the axis it needs to.
I've just done a lot of production work and you want your fixturing to be as easy and quick to use as possible.... like I don't know how you expect to get at the bolts for the parts in the rear? Take the fixture out of the machine? I think I would have investigated a fourth axis and used a tombstone for the parts.....