Most of you may be through the Aperture 2 to Aperture 3 conversion but for anybody still waiting or still facing difficulties here are a couple observations and some hypothesis regarding one of the big bugaboos - Endless Processing after conversion that hangs up other things you want to do behind it.
I was participating in a conversation over on the Apple support forums regarding something completely different and based on input from a few different folks ONE of the things that seems is the likely culprit at the root of Aperture 3's woes that causes this is a combination of file size and the retouch tool. That is to say - smaller files with a large amount of retouch points or large files with a limited number. After correlating this to my experience and observations it looks like this is absolutely a factor. Some folks are even having issues associated with this after the conversion was beaten into submission with new files.
Maybe one of the reasons my own library went so so smoothly is that I have no files that use the retouch/healing tool. None. All of the advice out there to make the conversion go as smoothy as possible is still a good idea and you may want to consider removing the retouch/healing brush from your images prior to conversion if it sounds like your images are in a high risk category.