Charlie,

This is what I have come up with.  (See the attachment) I still haven't finalized the setup.   

I am not sure about the low pressure filters, or how to tell which one might be plugging other than the fuel flow from that side would stop.  That would ruin you day.

The little loop on the return valve is to make sure that the return flow is not stopped when the valve is changed over.  I like the idea of being able to have control over where the return fuel is going and not having to worry about pumping fuel overboard, although you could if you forgot to change

I have also thought about draining the Aux tanks back to the mains but that would add two shutoff valves and remove only one of the 3 way valves.  

If you have got better ideas draw me a picture.