Install the filter after the pump, a simple pickup screen before the pump will be sufficient.
IIRC the s2000 uses a returnless fuel system, so the rail has only an inlet, no outlet or pressure regulator.
1) You can add an outlet to the rail and install the regulator after the rail and route the excess fuel back to the tank.
2) You can install 'T' the line after the pump, one line to the rail, the other to a regulator, with the outlet of the regulator returning to the tank.
#1 is the traditional, return, system.
#2 is essentially stock, the regulator and pump are housed in the 'pickup assembly' in the tank. You can install the same arrangement externally.
As for transfer between the tanks there are several ways that the OEMs achieve this with 'saddle' tanks.
1) Gravity/siphon with a transfer tube between the sumps
2) Low pressure transfer pump
3) Returned fuel jet siphon
#1 is the simplest, and it does work. Concerns of fuel leaks are over-thought, any fuel leak is bad.
#2 more parts, more weight, risk of pump failure should the slave tank run dry
#3 is my favorite. Returned fuel routed to the slave tank, and is sprayed through a jet into a transfer tube. It creates a siphon effect, pulling fuel from the slave tank into the primary tank. It's very similar to a transfer tube but eliminates the chance of an air lock.
Here's a 'large-scale' jet siphon, these are commonly used in rural fire fighting to transfer water between portable tanks.
Water is pumped into the small inlet on the right, water is drawn from the tank through the square inlet on the bottom and out through the larger hose to another tank. They will really move some water, IIRC 600+gpm transferred for ~50gpm input. I used to be an NFPA driver/operator but it's been a few years.