Apple lossless to a p99. I did some unscientific testing (using my ears lol), and I couldn't tell a difference between the ipod and cd.
I know the p99 is far from an 'integration' piece, and cost some good coin. But you'll need something to bypass the ipod dac. The pioneer will do that, plus many other great features in one package. I'm sure there are other solutions as well.
All depends on your budget, and goals.
Apple Lossless is a lossless compression algorithm. It is compressed, but no loss is made in doing so, therefore it is as good as the original and can in fact be restored back to the original. (i.e. = CD Quality, assuming you got a good rip off your CD to start with.)
To get a good rip to begin with, use Exact Audio Copy. This program will read your CD as many times as it needs to until it has a perfect rip. With a simple add on, it can be configured to compress using ALAC (Apple Lossless) and import into iTunes for you.