This is such a huge subject that I won't attempt to address all your questions at once, but rather address some of them now and maybe more of them later.
When you're starting on a job to rip 1000 CDs, you need to realize that you will be taking an enormous risk if you intend to store the resulting files without making backups! You are also going to need a lot of diskspace if you store the ripped files in an uncompressed format such as WAV.
By using a lossless compression format such as APE (Monkey's Audio) or FLAC, you will be able to reduce your storage requirements to roughly 50-60% of the requirements for uncompressed WAV. With the right tools you will be able to convert all your losslessly compressed files to any other format you decide on later on.
If you follow my suggestion to store your rips in a losslessly compressed format, you will probably be able to back everything up to a single external harddrive such as e.g. a 300GB Maxtor OneTouch II drive.
I know that EAC can rip and encode to APE format (my personal preference) out of the box, and it can probably also rip and convert to FLAC by configuring it in the right way - I'm not using FLAC so I haven't tried this.
EAC is going to give you the most accurate rips if you configure it to compensate correctly for the audio read offset of your drive(s). The only other tool I know of which can do this properly is PlexTools, which only works on Plextor drives.
If you don't care about correcting your drive's audio read offset, which is somewhere between a few samples and hundreds of samples (out of 44.100 samples per second), then there are other tools available which are more convenient than EAC.
I can personally recommend J. River Media Center which is shareware, and which is great for ripping, converting, organizing and playing music! Ripping and converting to the lossless APE format is one of many supported formats.
If you just rip your CDs to uncompressed format, the time will be constrained only by the performance of your ripping drive(s) and the ripping program and method; having the fastest CPU in the world won't make any difference.
If you rip and encode at the same time, or when you encode later, a fast CPU will definitely help, but depending on the encoding format it's possible that the ripping speed of your CD/DVD drive will still be the bottleneck.
If you use J. River Media Center for ripping (and encoding), you can use it with all your CD/DVD drives simultaneously if you want, so that you can rip and encode multiple CDs in parallel. If you are encoding while ripping, having a fast CPU or multiple CPUs will make this go faster.
When you rip your music CDs to files on your computer, you will realize (if you haven't already) that it's import to tag the files with information about artists, track numbers, song titles and so on. Many programs, including EAC and J. River Media Center, will automate this for you by looking up the information over your Internet connection. But if you want all information to be 100% correct, you are going to have to spend some time checking and correcting this information for many albums!!!
That's enough for now. I'll be checking back to this thread later.