Question

What phase in the Declaration of Independence might be considered by some to violate the implied constitutional principle of the separation of church and state

Answer 1

What phase?? Or do you mean what phrase?

http://en.wikipedia.org/wiki/United_States_Declaration_of_Independence#Annotated_text_of_the_Declaration

Since the Constitution was nowhere near written when the Declaration was written, signed, and published, I'm not sure how you could answer such a question.

And, finally, you need to keep in mind that the phrase "separation of church and state" is not literally in the Constitution. That phrase came from another source:
http://en.wikipedia.org/wiki/Separation_of_church_and_state

Let us know what you come up with to answer your question, and someone here will be happy to comment on your thinking.

=)