Your theory about the noise is very reasonable. Although a replacement comes with the steel crank gear they aren't a matched pair so a new fibre gear can be swapped in if you're happy the crank gear is OK. What might be happening could be down to the amount of wear to the bronze thrust plate. This will have an effect on how the teeth run together. The old fibre gear would have settled into the wear pattern of the plate and the new one might now be tight or loose. Slightly tight would be my guess. With luck it could settle down after a bit of mileage. In the mean time I don't think I'd thrash it too much!