I picked these four things out of your post because they caught my eye; I haven't the patience to to go through the whole thing.
'1. "From the day it took office, the Bush administration "dropped a shroud of secrecy" over the federal government."
Opinion - not "evidence" - I take it that the federal governments business in the previous administration was completely open and transparent- Is that what Mr. Krugman is trying to say? - if so I don't buy it.'
No, he didn't say that. The federal governments business in the previous administration was not completely open and transparent, but the Bush administration is more secretive. Check it out.
'2. After 9/11 - "Ari Fleischer ominously warned, "need to watch what they say, watch what they do." 'Sounds pretty logical and sensible thing to do - what would Mr. Krugman rather have had Ari Fleischer say?'
In the context of the time it was a threat. The prevailing attitude, and is, was that those who criticize the administration are helping the terrorists. Myself, I would rather hear him say "We do not need to give up freedom for safety."
'3. -snip 1 - Purely Mr. Clarke's opinion.'
True. Informed opinion, though.
'4. -snip 2 - Bush officials have not attacked Mr. Clarke's character. They have pointed out a number of significant inconsistencies in both Mr. Clarke's actions and statements. There is no independent evidence confirming the thrust of his charges, there is only opinion.'
What I have heard is largely variations on "disgruntled employee." But 60 Minutes said they had witnesses to at least one of Clarke's conversations with Bush.
Seems to me you are arguing to win the debate rather than to arrive at (an approximation of) the truth.