personally, I would always use individual 'p' clips to avoid the lines rubbing together regardless what the IVA man thinks. You can mount two 'p' clips on one bolt so no difference to the number of holes or bolts to do up.
There is loads of room in the tunnel above the gearbox and propshaft so just mount them high up on the side of the tunnel. I think under the floor or inside the passenger area just adds complications and potential issues.
I don't recall have any fluid inside my Facet pump so I wouldn't worry about priming it. I think its more important that the HP pump doesn't run dry so run your LP pump first to make sure the swirl pot is full before the HP pump starts up.
Propshaft, brake and fuel lines. by marlinpeter, on Flickr