well im stumped.

[Racing Rice]

When you bleed the system you have to make sure you have ALL of the air out of them lines. Its best to find a buddy and one pump while one bleeds. Make sure you keep fluid in the reservoir at all times. Also we always start at the wheel furthest from the MC. Thats the way we've always done it, and the way we were told to do it.

On another note, what do you mean you let the Master Cylinder get to low? Does the fluid disapper on its own or were you bleeding it when it got to low?

If it gets to low on its own, you may have a small leak somewhere. You maybe getting air in from there, or losing fluid from there. You should find it and fit it ASAP.