heheh, I've reached a blissful compromise with the whole Reader can't do PDF well issue. I picked up and installed the PDF convertor for the Words Gear device and PDF's look awesome on it. It sucked I have to shell out a little extra cash for this, but the PDF's are spot-on and scrolling doesn't institute whole-screen redraws; in other words, it scrolls just like on your PC screen. That being said, while I now have two gadgets to read books on, one it for plain 'ol books and the other suit my needs for comics, magazine, and techie books.
I know this doesn't help too much with the Reader issue and PDF's, but I'd suggest running them through either Rasterfarian or PDFRead. Both do a darn good job at making PDF's more usable on the Reader, though they're really hampered by the Reader itself in how it renders/redraws PDF's. Good luck, have fun, and welcome to the club!