Minimum one filter after the pump, before the engine. Your choice if you want it close to the motor (like most EFI Toyota's) or close to the pump (a la EFI JD-JE Camira). Under and next to the pump works, as does near the engine, and maybe easier to change down the track if its under the bonnet.
Run a pre-filter if you want to spoil your VL pump.
I have retained the standard filter on my GZE motor, fitted a Camira pump to the rear chassis rail on my RA23, and another filter in the half inch hose from the tank down to the pump. This pre-filter sits alongside the tank mounted via a bracket to one of the tank mounting bolts.
Run your power up into the boot, under the tank, down thru the cabin under the rear bench seat (use the existing holes) and then along the trans tunnel to reach where-ever you have your ECU. I'm assuming you are fitting this somewhere near the glovebox.
Mitch.