The brake and clutch pedals should be the same height.. Do you have the inside spring on the brake pedal to pull it to it's normal height?
As for bleeding By FAR the best way is to place a vacuume on the far end of the system and PULL the fluid thru the lines.
I am not aware of the rods into the master cylinder... as far as I know they are one and the same. Others may have experience with these.
Big Jim <img src="/forums/images/graemlins/pfft.gif" alt="" />

professional bovine relocation specialist