To test your theory that she was working on a story her editors rejected, we would need to know when her editors rejected her story idea. There may be notes on that. Once her story idea was rejected, she should have stopped seeing Libby. If she didn't then there may have been some other reason she was seeing him.
I need no additional evidence to fully agree with your answer to number 2. She is lying and concealing.
I wonder if, in fact, Judith Miller, invoked the Fifth Amendment before the grand jury.
I quote from an article on the internet by Solomon L. Wisenberg:
One of the most delicate tasks for the practitioner representing a witness or subject in a white-collar investigation is the tactical decision of whether to invoke the Fifth Amendment privilege against self-incrimination during the grand jury phase. This question can be even more complex in the case of grand jury subpoenas for documents. Two recent decisions by the United States Supreme Court, Ohio v. Reiner, 532 U.S. 17, 121 S.Ct. 1252 (2001), and United States v. Hubbell, 530 U.S. 27 (2000), indicate that its current members share, for the most part, an expansive view of the Self-Incrimination Clause. These decisions should be used aggressively during the grand jury stage whenever counsel needs to shield the client from having to testify or produce potentially incriminating documents.
The Fifth Amendment provides in pertinent part that "
o person . . . shall be compelled in any criminal case to be a witness against himself." A long-standing precept of Fifth Amendment jurisprudence is that the privilege applies to any statement that might tend to incriminate the witness. The statement at issue need not directly implicate the witness as long as it "furnish a link in the chain of evidence needed to prosecute the claimant for a...crime." Hoffman v. United States, 341 U.S. 479, 486-87 (1951). Another venerable precedent holds that the privilege protects the innocent as well as the guilty. Grunewald v. United States, 353 U.S. 391 (1957). Reiner strikingly reaffirmed both principles in the context of an Ohio criminal trial. Though it did not pertain to a grand jury proceeding, Reiner can easily be applied in that context.
http://library.findlaw.com/2005/Jan/19/147944.html
I have no evidence that she did invoke the Fifth, but I have wondered if, assuming it is true that she struck a deal to limit her testimony with Fitzgerald, a threat on her part to invoke it might have caused him to agree to the deal. Of course, it is more likely that Fitzgerald only needed to know about her conversations with Libby and already has enough evidence on others. It may also be that his contempt order focused on the Libby information. I don't know.