Chris, it sounds like the lack of a choke is what's keeping the car from starting. If the choke plate is still there you could get a cable and make it into a manual choke.
As far as the well being blocked off, it's actually the heat crossover passage from one head to the other the racers block off to keep the intake manifold cool. If it were mine, and it's a daily driver, I'd get the automatic choke working.