If you could find a way to do the 5 speed swap now instead of rebuilding the 440 I don't think you would ever regret that decision. Even when you factor in the additional cost.
It changes it into a whole different truck.
You know mine had that same whine just before the transmission completely failed. Nothing I did could save it. Currently in the process of swapping in the 5 speed. Rebuilding the A440 just didn't give me a feeling of confidence.