Problem upgrading Aperture 2 to 3

I have been using Aperture since version 1. Today I downloaded Aperture 3 from the app store. That changed Aperture to version 3 in my Applications folder. I opened Aperture and it had me chose to update my Aperture Library. It kept my original (version 2) library and made a totally new library which is a little bigger than the old one. During the processing Time Machine activated and I presume tried to copy the new Library but aborted because of lack of disc space. I also got an Aperture error message that it had to correct something and I had it procede. I shut off Time Machine and Aperture 3 eventually opened.
Help, all the images seem to be there but all my projects, folders and most ratings are gone. I now have a massive unorganized Library which is of course a disaster involving years of work.

Thanks Tony.
I ended up restarting my computer, turned off Time Machine and then reopened Aperture. It asked if I wanted to upgrade my library and I clicked yes. It then updated my library for a few hours. All my projects, folders, etc appear to have returned intact.
I think Apple ought to recommend turning off Time Machine and energy saver when upgrading a large library.
One problem that I have now noticed is that a number of images I adjusted in earlier versions are now way off. These are images I did RAW adjustments to in Aperture. At the top of the Adjustments tab it says: "This photo was adjusted using an earlier version of Apple's RAW processing". There is a button there that says "Reprocess". When I click that it doesn't solve the problem.
Versions of the same images I edited in Photoshop and have the little photoshop icon look fine. Aperture 3 appears to have run the contrast slider up all the way so the images now look terrible. So it seems the problem is in Aperture 3's updating of my Aperture RAW adjustments. But it's not all of them. Some images look fine.
I hope I don't have to go back and correct them all. Am I missing something?
Bill

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