Your CD-Extra actually isn't a CD-Extra, but a mixed mode CD... anyway:
1.Rip the audio tracks with EAC.
2. Rip the data track with ISOBuster.
3. Create a REAL CD-Extra, putting the data track last. I believe that Nero can do the job, although I don't use it. But I can assure you that RecordNowMax, Padus Discjuggler and Pinnacle Instant CD/DVD can easily create such disks, with CD-Text and ISRC/UPC codes, plus custom pregaps (including of course zeroed ones). I have burned many CD-Extras with those three applications on different burners (Lite-On 24102b, Plextor 24/10/40, Plextor Premium, Sony DRU-500, Toshiba SD-M 6112) and excluding few cases of insufficent burner driver support, the result was fine.
The revolution cannot be a lever, or an essay, or tablaeu, or embroidery. It cannot proceed mellowly, piece-by-piece, gently, devoutly, simply and humbly.
Mao Zedong