They should all be at the same setting. Turn them in, just till they seat. Count the turns. That's the setting the rebuilder set for you, I suppose, and is likely the book value for the stock filter and exhaust.
Judging from your problem description and the way mine behaves when they are out too far. I'm guessing that you will need to turn them in a bit to compensate for the lack of air filter restriction and resultant vacuum in the carb throats. (It would be nice to know your spark plug deposit colors.) Any way, turning the screws in should help enrich the slow jet mixture and improve the bottom end response to compensate for the lack of strong draw from the venturi. As I said earlier, a relevant test would also be to apply partial choke to see if the throttle response improves. If that helps, you then know that you need to enrich the mixture.
Cheers,