IMHO, stainless steel is one of the most difficult (if not THE most difficult) material to work with for brake and fuel lines. The hardness of SS makes it more difficult to get leak-free connections as compared to softer metals. If the leaks are on the smaller/slower side, you may be able to resolve via loosening and tightening several times....helping the metal to take a "set" within the connection. It also helps to do this with the fixture unbolted from its mounting point (e.g. leave the Master Cylinder unbolted, or at least loose, on the brake booster when tightening the front and rear lines to the MC.) This will help ensure that the incoming/outgoing lines have optimal geometry WRT the fixture they are connecting to. This is particularly important when working with a non-malleable material like SS.
Just out of curiosity, what style flares did the brake line kit come with? Also, did you visually inspect all your original hardware (tee connections, prop valve, etc) before installing the new lines to ensure you had no damage on any of the nippled connection points?