I think the tests were undertaken to eliminate fouling between the flaps and the ailerons as a possible cause of the accident. The investigators needed to consider all possible causes of the uncontrolled bank, in addition to an aileron roll, an asymmetrical extention or retraction of the flaps, could and probably would have produced forces that could not be controlled by the ailerons. It has happened on other aircraft designs. I well remember my flying instructor insisting that a visual check to both sides of the aircraft be made whenever the flap lever was operated. One of the things I used to regularly forget, especially selecting final stage flap just before landing. I knew the flaps on either side were mechanically connected, what could go wrong? Well they were connected with a joint that was capable of sliding and rotating. Copies of accident reports in the office soon persuaded me that it was a vital safety precaution to carry out a visual check in a small aircraft. Larger aircraft are not much different, things just happen at a different pace and control surfaces may not be visible from the cockpit, so you have to rely on other telltales.
So you are correct when you say that a flap fault could have produced similar results, but the solution is to return the flap lever to the position it was in before the flight upset started in order to restore a balance. Takeoff flap settings are usually only a few degrees and designed to increase the effective wing area while keeping drag at a low level. If one of the flaps had dropped completely, commanding full flaps would have rebalanced the aircraft to a level attitude and given the impressive power to weight ratio of the Electra, it should have been capable of maintaining altitude even with full flaps set.
Witness marks on recovered components suggested that takeoff flap was set and maintained throughout the flight and that the flaps were not set asymmetrically before impact.
All the additional tests were conducted to eliminate other possible causes before settling on a break in the aileron control cables as the cause of the accident. Of course the root cause was the incorrect actions of the maintenance engineers on the ground.
Were there indications of a potential problem during the takeoff run?
The rolling takeoff is significant in that it is usual to stop, verify runway heading and compasses are aligned and that all controls are free and move to their full extent. There is mention in the report that a test pilot felt virtually no change in the feel of the controls when the aileron cable was deliberately severed on a test rig.
If the full and free control movements were conducted on, or just coming off the stand, perhaps the aileron cable separated during this test. The trip along the taxiway to the runway would not have involved movement of the ailerons, just toe brakes, throttles and rudder.
The first indication that the pilots might have had that something was not quite right would probably been just before V2 when they were already committed to takeoff. Up until that point, the rudder would have been the sole directional control in use. Perhaps the aircraft did not respond correctly at that point to aileron input to counter a slight crosswind. At that point it could have been dismissed as slop in the control rigging, since the aircraft had a history of poor aileron response. It was only once the right bank on departure was initiated and could not be countered, that it became obvious that this was a critical failure in the control system. The accident report suggests that the pilots would not have been aware of the cable disconnect through any difference in feeling of the control yokes, only that the aircraft failed to respond to aileron control inputs.
The general rule is that once an aircraft has reached flying speed it is safer to lift off and try and solve problems once airborne than to attempt to stop. This was one of the exceptions to that rule.
The rolling takeoff may have contributed in some way to the accident, but that would rely on a visual check of the aileron movements being conducted from the cockpit and the lack of proper movement being noticed. I suspect that wing visibility from the cockpit is very limited if possible at all, like most larger aircraft.