I remember reading a thread about how you should break in a newly rebuilt engine here in the past few months... you may want to do a search for it... they said it was crucial for ensuring a good long lifespan of a diesel engine.

As far as purging fuel... Lubro Moly has a product where you disconnect some fuel hoses... stick them in this products container and wa-la! Clean fuel system. I bought a can of the stuff but just don't know enough about purging systems to use it... it says for "professional use only"

Question: Did you prime the system with the fuel pump?