(Cockpit lockers are water tight and secured, additional drains have been installed in the cockpit and I had put the companionway boards in earlier so they were draining quickly and to me posed no real threat).
IMHO, this was the most important action that you took. I see very experienced sailors who neglect to secure the hatches and install the hatchboards when the going gets rough, and it is very common to see people who don't think to secure the hatches to cockpit lockers. In the severest conditions, when waves are breaking over the boat and into the cockpit, if you can keep the water from flooding into the interior of the boat, the boat will retain it's buoyancy. I recently saw a boat that sank immediately when it was knocked down with the hatchboards not in place. Nothing is more important than keeping the boat sealed, like a corked bottle.
Now, on to my biggest mistake. What I think I should have done is maintain sea room and continue to run as I had control....
I agree. You suggest that you had sea room, so I'd suggest taking down all sails and running downwind under bare poles, with the aid of the outboard motor. If your motor has a long shaft, it shouldn't cavitate significantly when running downwind. I was caught in a severe microburst, and was running parallel to an outboard-powered Cal 25 that used that technique, and he (and I) made it through conditions that sank a much bigger boat in the same storm.
Small sailboats have a surprising capacity to survive, as long as you keep your head about you, keep them buoyant, avoid damaging broaches or capsizes, and stay with the boat.