These digital files will be my main source of music and I want the information in these files to be EXACTLY the same as is on the CD. Ie. There should be no difference between playing the CD or the imported digital file through the same DAC. Is this achieved with lossless compression?Lossless compression is a necessary but not sufficient condition. If you want an exact copy then you need either some way of verifying that it's exact, or if that's not possible take all reasonable steps to try to ensure that it is. On windows the approach is generally to use EAC (exact audio copy), which is a plugin for some media players (dpPoweramp is one I think), which creates a checksum of your rip and compares it to other people's, giving you a level of confidence that your rip is exact. On a Mac, EAC is tricky to implement and your best bet is to use iTunes with error correction turned on - this is the approach I use and it's served me well, but I can't be 100% sure that my copies are 'exact'.
Does the computer/sound card affect the imported file?No, if you take one of the the approaches listed above. If you do not, you can be at the mercy of lesser quality CD drives producing poor quality rips. The soundcard is not involved.
Does the importing software affect the resulting imported lossless file?In my opinion, no, though only iTunes uses a licensed version of the apple lossless codec - any other is using a reverse-engineered one. And if you extrapolate that, it's possible that different players may implement different WMA or FLAC codecs...
Is there a difference in apple lossless or wav?In my experience, no.
Are there any other options I should consider?Depends on both your OS and what you want to stream it with. If you're on windows, FLAC and WMA lossless are alternatives to apple lossless, both of which support tagging, as are AIFF and WAV, which don't (or at least I know WAV doesn't, less sure about AIFF), and neither of the latter are compressed so you need a lot of disc space. Which option is best depends on what you want to play it with, since some formats are supported by some clients and not others. Got any ideas about whether you might use airport express, uniti, squeezebox, windows media extender etc etc?
Does converting between lossless files affect the data ie. (if I convert a wav file to flac, convert this flac to apple lossless and then convert this apple lossless to wav, will the two wav files be exactly the same?)That's the theory, yes, and there's plenty of evidence out there of people having done this conversion and comparing file versions before and after and ending up with the same result down at a binary level, but I'm kind of going to take everybody's word for it on that one as the results I'm getting are pretty damn good and life's too short.
Responsible for the techie bits. Has biased opinions.