I'm trying to work out a way to offer re-design help to members, but we're not there yet.

Right now, what I'd recommend is get to leave the plumbing alone, for the most part, but get the timer and sand taken care of. You just need 1 more union (pressure side of multi-port, near filter) in order to lift the multi-port valve. Having the messed up back wash, makes it easy for now.

You can install this check valve:
King Brothers Inc. KC-1500-S 1-1/2-Inch Slip PVC Schedule 40 Spring Check Valve, Gray @ Amazon

to assure positive pressure at the suction inlet of the Polaris booster. If you do, you'll need to remove the Rainbow feeder and check valve -- if that's the old 10# spring valve, it's a VERY significant energy waster! If it's a newer model with a light spring, then you won't need the check from Amazon, since the Rainbow valve will assure positive pressure at the Polaris suction.