For the 24/96 audio, you can burn a CD24:

http://www.alesis.com/support/faqs/masterlink.html#g3

What is a "CD24"?

A CD24 is a special kind of Compact Disc that can be made and played by the Alesis MasterLink. It allows you to store audio at higher sample rates and word lengths than is allowed by the standard consumer "Red Book" CD format. A CD24 can also be played in a computer's CD-ROM drive as long as your soundcard and software can handle the resolution.

How can CD24s be read by a computer?

Alesis CD24s follow the common PC and Mac-compatible CD-ROM standard ISO 9660, and the audio files on the disc follow the AIFF format readable by almost all higher-resolution audio software.

AIFF is the Apple version of the uncompressed PCM Windows .wav format. I'm not sure if these discs will be read by Windows as wavs or as aiffs. All you have to do is go to start > my computer > click on your CD/DVD drive. No special software program is needed. Then select all the files and copy them to a folder on you hard drive. There is no "digital audio extraction" or DAE like what is done with ripping audio CDs with EAC, because these are data discs. Data discs copy much more reliably than audio CDs because they have built in error correction. Maybe you can just change the file extension from .aiff to .wav for each file. Then you can compress the wavs to FLAC with Trader's Little Helper.

For the CD-quality 16/44.1 audio that has been burned to audio CD, you can rip them into .wav format with EAC and then compress to FLAC with Trader's Little Helper. I think EAC is capable of ripping directly into FLAC, but I have never done it this way. I find it to be much simpler to just rip CDs into .wav and then compress to FLAC with a separate program, like TLH or FLAC Frontend. It would be good to configure EAC's read offset, use secure mode to rip, and save the .log file that is generated as proof of an accurate error-free rip.

If you can burn the 16/44.1 files as ISO 9660 data discs, like the CD24s mentioned above, that might be better, because you won't have to bother determining the read offset of your computer's CD/DVD-ROM drive. It might be worth it to configure the read offset anyway so you can make perfect copies of any commercial audio CDs. I'm don't know if the write offset is corrected on the Masterlink's burner when it burns audio CDs. If the discs are burned as data, the offsets are not an issue.