Earlier today, I spoke with a tech at the Canon service center in Irvine. It turns out that its location is more like 2+ hours from me so finding that kind of time to go up there is a bit of a challenge.
First off, the tech told me that every camera is checked before it leaves the factory and if the sensors are dirty, they don't ship them. He claimed that it could not have left the factory that dirty. It may be a company line, but the truth is I didn't own the scope before I bought the 40D and started shooting with the camera, so I'll not devote any mental energy toward that until I buy another body, which may be a 1D Mark III, but that's another story.
I spoke with the tech for about thirty minutes, he was very professional. When I told him that I had taken perhaps 2000 shots within the first two weeks, he was not surprised. He agreed that it is entirely possible that the parts within the camera may be "breaking-in" or "wearing-in" and could have been partially responsible for so much dust in under two weeks. His comment, however, was not that two weeks was the issue, but that 2000 plus shots had been taken. He was very insistent that I bring the camera in for a look-see, but said that if I tried to clean a sensor with swabs and fluid myself, I would void the warranty. I'm not sure if the service center could ever tell if I did or did not clean it myself, but we'll see. The tech also reminded me that in SoCal, we live in a very dry and dusty climate and that they see dirty sensors all day long. One other thing the tech said was that their inspection would determine if there might be some parts that are wearing incorrectly that could be the cause of the problem, so again he implored me to bring it in.
I did ask the tech how they clean sensors and he would not reveal their methods to me, other than to say that what they do is entirely different than any third party company like Delkin or PhotoSol could provide an average Joe like me.
At the end of the call, I told the tech that at this time, I could not see much anything with my scope, but was seeing ten or so blobs at f22 and beyond. He said that those types of spots are usually dried liquid, which would lead me to believe that PhotoSol's E2 might not be the way to go with a 40D. Perhaps Delkin's solution is better? Has anyone out there used Delkin's solution? They claim it will work on any sensor in any DSLR.
To sum it up, the tech said that I have a very high-end camera with a high fps rate and should take advantage of the 1 year warranty, which includes free cleanings. Of course, assuming that I or some local shop has not already tried to clean it. I wonder if they can tell if the end user or local shop has swabbed the sensor? Any thoughts there?
I would like some instant gratification on this issue, but we all know that's not reasonable. I'd love to drive to Irvine tomorrow, but I cannot.
Given that my sensor is at the moment, mostly clean and that I don't see the blobs below f22, I'm going to shoot for a few more weeks and see what develops.
I posted some images in my original post. Based on those I feel that I have a good copy of the body, would anyone disagree?
Thanks again, I'll be posting more images soon and be scoping the sensor to see if it again gets out of hand so quickly. If it does dirty-up like it did before in a short period of time, I'll make the time for the day trip to Irvine.
At the end of the day, I wish that I had purchased the body locally. I could call the very reputable company in New York that I bought it from and get an RMA and request another body, but quite frankly, I don't want to. In spite of this one frustration, I love this camera so much, I don't want to put it down! I'm guessing many folks out there would also want to keep their new toy home. I guess it is a good problem to have. 
Best,
-Michael