Secondary filter can be mounted at any elevation/height. Just figure out where you want it, measure what length hoses you will need to locate it there (keep it in the same "order" in the fuel system)-- probably easiest to have new hoses made that attach to existing hoses and go from there to the new location.
Probably most convenient to have the two filters next to each other. But, the lift pump is between them in terms of fuel flow.
And the manual primer pump is available straight, with 45 degree adapter and 90 degree adapter.