1) Do you think the Bush Admin. helped or hurt the amount of CT's that surfaced after 9/11? Did they bring on a lot of this themselves?
I don't like your wording, so I'll say that the administration's behavior after
and before 9/11 contributed rhetorical fodder to conspiracy theories concerning the 9/11 attacks. The administration's behavior from about the 2002 SotU forward, with much emphasis on the run-up to Iraq and the invasion (and subsequent lack of WMD), tended to alienate a great many people throughout the world and sparked paranoia like a match to flash paper.
2) Knowing what you know now, what would you have done different to insure/prevent CT's after 9/11? What did Bush do/not do, that brought on more CT's?
The first and foremost thing the administration could have done was to be openly and publicly supportive of the 9/11 Commission when it was initially forming and requesting funds. The initial resistance and constant undermining of the Commission that took place has left an indelible negative mark on an otherwise thorough investigation. Another thing I would have suggested differently was the whole "Axis of Evil" thing in January of 2002, most especially because one of those 'Axis' members (Iran) had actually been helping us with support (money and influence) in Afghanistan. That, along with the fact that not a single shred of evidence linking Iraq in any way to al Qaeda (at least not as a friendly) or 9/11 was ever found but continually implied through pro-war rhetoric by White House officials leaves quite a bitter taste in the mouths of many Americans (and not just conspiracy theorists). It would have been better for the administration and for America in general if things like the August 6th memo, the Tora Bora incident, and many things that Richard Clarke talks about later in books came up in a more explanatory format while there was more sympathy for the US and the administration worldwide. Yes, there would have been some embarrassment, but what most likely what would have followed may have been precisely the calls for improved intelligence-gathering resources and integration that the administration so ham-fistedly pushed through in the first place. Also, a much-overlooked detail is that the administration shouldn't have allowed Christie Whitman's office to 'edit' facts about the Ground Zero dangers and should have pushed both the EPA and FEMA to be more aggressive about on-site safety of the clean-up. Unfortunately this would have cost more and it would have meant things like Wall Street and many offices having to relocate for longer, but considering the lasting effects that such concern would have for the administration's credibility it would have been worth it.
Other than that, additional things I think would have helped are avoiding some of the more blatant nepotism (like in the Justice Dept.) and not beating the war drums against Iran (especially not to the same tune as Iraq just a few years prior).
3) If the Bush admin. had been completely transparent, would that have completely prevented 9/11 truth from surfacing, or would it have happened anyway?
Do you often completely talk in such complete absolutes? Would 9/11 conspiracy theories have been totally avoided? No, absolutes are silly. However, the vast majority of the compelling talking points truthers use to attract people would have been nullified by a little more due diligence and a more open policy of addressing and answering questions regarding the attacks. Many of the truthers I've spoken with these last couple years tend to have the crux of their views on the Iraq War, on information that's come out from "leaks" or other sources contradicting the administrations "we knew nothing at all" claims prior to the attacks, and by information about the health problems facing construction and cleanup crew members from Ground Zero. Those are three talking points that are actually featured heavily in LC:FC, and despite the nuanced facts regarding them that do not support a conspiracy they are easily presented in a conspirational manner because of the closed-lipped behavior of the administration and the fact that parts of the administration have been caught in some egregious falsehoods.
Some of the qualities of the administration that lend to conspiracy theories aren't exclusive to the Bush administration, though. Politicians seem to habitually avoid simple admissions of error or straight-forward apologizing, and it seems to be a quality more stark in politics today than it was 10, 20, or 25 (or more) years ago. Of course, that's more a subject on politics than it is on conspiracy theories, so I won't try to give too detailed an explanation of what I mean except to say that since Nixon it seems like every subsequent administration (Dem. and Rep.) has had more and more difficult a time with being frank and honest with the American people. When things aren't going poorly-- no wars, decent economy, not a bunch of scandals-- that quality tends to be the brunt of jokes and comedy skits. When things start seeming more stressed-- two wars, a shrinking dollar, and a current financial crisis-- those jokes and comedy skits can tend to hit tender spots and (for some) stir varied levels of distrust in our government in general. Conspiracy theories can be an extreme example of such distrust. CTs can also be indicative of severe paranoia issues, but I posit that the majority of people who believe in conspiracy theories are of that opinion because of the extreme distrust I mention above, not the severe (or clinically acute) paranoia.