in the committee. He had the entire committee and spouses to a dinner party and by February 5th, he had his first round table (on Afghanistan). I agree with you that the DK comment and others, including one at a MA talk, where he joked about being chair of the committee while he could still talk without drooling - something he had not expected as there were so many people with greater seniority was one. In the MA townhalls, he was already speaking of hearings and investigations.
I think you are right on the SoS, but I suspect that he was always somewhat conflicted because of Kennedy's illness. Remember the article on Kennedy in the summer of 2008 speaking of Kerry's potential legacy (in the Senate), that had to mean Kennedy was lobbying for Kerry to stay in the Senate.
http://www.democraticunderground.com/discuss/duboard.php?az=show_topic&forum=273&topic_id=158814 I doubt Kerry would have dismissed Kennedy's comments out of hand - not to mention the fact that Kennedy was right (even without the SFRC chair) Kerry was very well positioned in the Senate.
What does not ring true is that Kerry lost the position because he lobbied too hard for it. This implies that he would have gotten it if he hadn't pushed for it as hard and that is ludicrous. It looks like Obama well before he won wanted HRC in this position - for whatever reasons. (I suspect the story that he offered her this in September is true and Biden's claim he had the choice of VP or SoS was Biden speaking through his hat.) Kerry had every reason to expect to be asked - Obama did owe him big time, he had excellent credentials, and he had done a brilliant job as the main foreign policy surrogate on the campaign - far better than the muddled job that Biden and Holbrooke each did on his campaign. This is why the media, which never does him any favors, listed him as the odds on favorite. (They also use that to imply that the diplomatic Kerry is tone deaf enough not to know when to stop and play into the "he's too ambitious" line that seems to apply only to JK.)
Thinking back to your TPTB Taibbi article, I suspect that Obama might have had intense pressure, not from Kerry, but from TBTB. Some of them had pushed HRC since 1992. The fiction that she meekly paid her dues as a Senate backbencher and had emerged as a power in the Senate was ok as long as she had the future of the Presidential run. The difference in her position in the Senate and her position with the power elite was a problem. If anyone had high powered lobbying behind him/her, it was HRC and it likely was before he won. (Remember that her team was even suggesting a co-Presidency in June when she was refusing to concede.)
As to Biden's comments, I have the same problem I always have with his stories. They always show himself as the wise, knowing person and diminish the other person, but not enough to justify any reaction. I used to think it was that he felt he needed to build himself, but you would think that as he was lucky enough to get the VP, he would stop doing that. Remembering the "sibling" analogy, this suggests that Biden still feels some need to flatter himself at JK's expense.