2001 Ford F350 trouble starting

I have a 2001 F-350 powerstroke, auto 4x4. Last week while trying to start it was making a clicking noise from under the dash. It was a relay in the fuse box, I took it out and replaced it and it quit clicking and started. Now while cranking(but not every time)I here another clicking noise under the dash(above the pedels) but not in the fuse box. It will not start as long as it is making the noise, it just cranks and cranks. I can return the key to the off position and start over and it starts fine?