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"I copied them over to Flash (CS3) as vectors and resized them" - what do you mean you copied over to Flash? Do you mean import?
"text I added myself doesn't look as good as it should" - check your anti-aliasing in Flash
"I'd prefer to keep the site at 800x550 resolution without rescaling but as you can see that isn't a good idea." - no, actually that is a good idea - not to rescale - any time you resize a flash document with rastered graphics, you will get distortion
'uses very small text (in the case of the menu on a black background) yet looks fine." - they are using pixel fonts
"Also, the thumbnail on the Portfolio page looks very bad even though it wasn't resized in any way using Flash (I reduced the size of the original image in Photoshop and changed the DPI from 200 to 72, then imported it into Flash as a jpeg." - looks fine to me (on the unscaled version), but I don't have anything else to compare it to - check your image compression settings in flash (both under Publish Settings/flash tab and when you double click the bitmap in the library you can control compression settings. What level of compression are you using when saving from Photoshop?
The word "graphic design" looks better here http://www.lotusgraphicdesign.net/ then here http://www.lotusgraphicdesign.net/small.html , but they are different sizes. Which is the original size?
Another note: "Because I was working with content already created in Illustrator (10), I copied them over to Flash (CS3) as vectors and resized them." if you actually imported an ai file into flash, I know it also imports clipping masks and things of that nature. When you resize an imported ai file, you may be getting weird results from also resizing the clipping masks, too. When I import an ai file, I break up everything as much as possible. Depending on how you import your ai file, bitmaps will be created, so make sure you stay away from bitmaps when possible when resizing any symbol.
That's all I can really think of.