ya, AI - Adobe Illustrator - files are vector format files, however flash cannot open them directly. You'll have to either
1. Open the logo file in Illustrator, open your flash file also in Flash. Copy paste from illustrator to flash program. Easy enough.
2. Use the export option in Illustrator to export as swf, then import that file from within Flash.
PSP is Paint Shop Pro? If it is, i think that is mainly a bitmap only program, no? not sure it handle vector format at all.
Anyway, if you dont have access to either Illustrator or Macromedia Freehand, then i suggest you use the provided bitmap for your animation.
If you dont resize you image it should look a-ok. Or if you resize from small to original bitmap size - final state, no jaggies.
Font use should be consistant sitewide.
The original logo font is Eurostile Extended Bold if i'm not mistaken, that or Bank Gothic.
The Main logo on top left hand corner, should link back to the home page, 'cos everyone's use to it that way.
Back to intro flash, The shape tweens doesn't look so good man, really, just fade-out first line and fade-in the next, you know, like they have it at the start of movies sometimes. Fade-in and fade-out, simple but classy.
You should definately rework the intro flash, its too far from 'pop-ing'. You can choose to remove it you know, and have the intro placed on the home page instead.