I agree, this is possibly the problem. If the throttle disc is open past the idle and transition holes, they stop working as designed. The disc should be between the holes at idle.
1. Increase your initial spark advance by 5-10° (and deduct this amount from your mechanical advance curve to achieve the same total), which will raise your idle speed and allow the speed screw adjustment to be relaxed and lower the throttle disc. It may also increase throttle response.
2. Drill a hole in the throttle disc close to the idle/transition holes. This allows more air to enter at a lower throttle disc angle, which will properly mask those openings. Typically, the hole is 3/64" to 5/64".