We got it done. Once the fan was lowered away from the ceiling I knew to what wires the new light is to be connected. The only difficulty we ran into was attaching the light's bracket to the ceiling. The metal box in the ceiling had one side going further into the ceiling than the other, preventing the bracket from being level when attached. I noticed that the fan used a much longer screw on that side so I used that screw with the bracket and it worked.
Yes, ceiling boxes sometimes not being level (flush) to the ceiling will present a challenge. But in the case of a light fixture it does not play much of a role. As long as the light is secured properly, the conductors/wires are not jammed in the light fixture box tight and the light operates then I guess you are good to go.