C,
Wow!!! That is one hot mess you are trying to fix...
I know this might not be what you want to hear, but I think that you would be much better off removing a little more concrete and re-plumbing like today's pools.. I mean your 75% there already..
If this were my pool (and I was 30 years younger) I would take out two feet of concrete right in front of the pump and filter.. This would allow you to remove the pump, the filter and heater and re-layout the plumbing so that you could have a true, Intake and Return valve setup needed for a Pool and Spa combo.
What you want to end up with is an "Intake" valve at the input to your pump that allows you to select suction from either your Spa Drain or your Skimmer.. And after the heater you want the "Return" valve that allows you to return the water to your Pool or to the Spa Jets... Easy for me to say but a lot harder for you to do, I'm sure...
I would cut the concrete back so that you could surround the equipment pad with river stone, so that it had a place to drain and where you did not have to bring any pipes up through the concrete.
Thanks,
Jim R.