Tim -
the CD reader does not impact quality (so long as it works) because it is reading data files not pits - that's the big reason that a hard drive transport sounds so much better then a CD player - none of the electro-optical-mechanical problems, and nothing happening in real time.
I have ripped some 2,000 CDs to Apple Lossless using the CD/DVD reader built in to my Mac tower. There does not appear to be any reason to buy a separate transport - though of course you can. I would recommend buying a SATA one to ensure that it is no slower then your built in.
BTW rip speed varies by CD and is software controlled - there is no option to set the rip speed as there is when you are setting up to burn a CD (eg 4x-8x-16x etc)
As to your choice of format - while AIFF (a 1988 Apple format) and WAV (a competing MSFT format) look good on paper, they offer no increase in quality and have some significant disadvantages.
You can spend about 5 minutes on Wikipedia and learn all about the various formats. And you can spend hours here and on the Asylum reading threads as person after person comes to understand that Apple Lossless or FLAC will return a bit perfect WAV or AIFF copy everytime.
The issue here is that neither WAV nor AIFF were designed with a file structure to support the kinds of database applications we use to manage our libraries. This is the realm of metadata and specifically "tags" - all the info about the recording which you can use to sort and select, as well as the album cover art. Because of the file design, this data gets lost in WAV and AIFF defeating a key benefit of this approach; instant access.
Personally I agree with Reubent - KISS is the way to go - nothing beats Apple Lossless in iTunes on a Mac. Lots of PC people have bought Macs specifically to run their music libraries and are thrilled that they did so. There are some alternative ripping softwares for the Mac but nothing that seems to offer enough benefits to have gained any traction. MAX is probably the leader but IMHO why bother. iTunes is one of Apple's crown jewels. It integrates all of the functions that you need, and is supported by a team of developers.
One of the real mantras of a hard drive based system is rip once, use many. iTunes also supports iPods, iPhones, Airport and Apple TV. For the last several years I have made the point in posts that going digital goes beyond audiophilia - it is a lifestyle choice.
If you are a died in the wool PC guy, you are into the realm of EAC, FLAC, Secret Rabbit etc. Point being that you have to roll your own and act as your own integrator. While I am sure this is more straightforward then it was even 12-24 months ago; its not easy and is not recommended for computer newbs or the faint at heart.
Beyond the problems of disc reading, the second achilles heel is SPDIF which is prone to a host of implementation problems. Whether you choose a Mac or a PC based solution, to achieve the maximum benefit for a hard drive transport you should use USB to get the data out of the computer to the DAC.
In addition to the excellent DACs recommended by ReubenT of which I have owned several; you should consider something like the Keces 151 which is a 10th or 20th of the price. There are a number of very innovative, very high quality DACs coming out of Taiwan and their performance is astounding.
