I don't think it matters which of the three nipples you attach the hose, I would go for the one that fits the hose the best. A couple of questions for you,
1. Where are you getting your vacuum from? Rear of carb or directly off the manifold?
2. Can you pump up the brakes and get a better pedal?
Pictures please!
Last, please give us a detailed description of how you bled the brakes.
C