I saw this thread from a google search so I too tried getting it to work
Hurdles: Recognizing the cdrom, second disk on installer, Registration, Recognizing Interlink

using FC6, wine-0.9.27

Recognizing the cdrom
easy fix create a link in ~/.wine/dosdevices that points to your cdrom's mount directory like so
ln -s /mnt/cdrom ~/.wine/dosdevices/d:

second disk on installer
easy easy fix don't cd to the cdrom directory
I installed from my home directory like so
mount /dev/cdrom /mnt/cdrom
wine d:\\SETUP.EXE
(then when it asked for the second disk I ran)
umount /mnt/cdrom
(installed the second disk)
mount /dev/cdrom /mnt/cdrom
(and clicked continue)

Registration
I had to look at a windows installed shortcut to find this one out.
I launched the launcher as follows
wine ~/.wine/drive_c/Program\ Files/Common\ Files/KnifeEdge/Launcher.exe REALFLIGHT3
I entered my keys and registered just fine :-)
I even upgraded.

Recognizing Interlink
I'm at a loss on this If I could figure this out I think I'm home free.