Need a little more info please. When you say when the brake is applied, do you mean when you are shifting from park into reverse or drive? Or do you mean when you are driving? If it is while you are shifting from park into a gear, then thats when you are putting a load on the tranny, and could be the pump, converter or hard parts in tranny. If its not a constant noise, then it could be u-joints. If its when you are driving and you brake, it is most likely not the tranny. Hard to make a diagnosis like that without experiencing, so your best bet is to probably let a tranny shop mechanic test drive. Be careful though, I was in that buisness many years ago, and there are some shady people there. Get a shop with references from people you trust. Try this. Hold foot on brake in park and shift into gear and note any noise. Then drive and brake several times at different speeds noting exact noises at each time. Post back results and hopefully someone can steer you in right direction. Good luck on your resto, the first one is always the most fun.
