If the problem brake bled better with the engine running, I would look for a vaccum issue with the power booster. I'm not sure what engine you have, but on the 4.2 there is a vacuum line from the upper intake to the power booster. I have had vacuum issues on mine in the past and have usually found a cracked or carbon blocked lint to be the culprit. I have a buddy that's a genious with these types of problems. If replacing the line does not help you, I can ask him to post some help for you because any advice I give you would just be a guess. Let me know how it all works out. Good luck.
1998 Ford F-150 XLT Flareside, 4.2L V-6, 2WD, automatic xmsn.