C.F. - if the audio CD is not copy protected you can do use the "copy" function, it has the same audio read error recovery functions as DAE (see the preferences in PT). if the CD has copy protection, you may need to enable "single session" under Drive Settings and rip it using DAE.
sorry can't help you with EAC, i don't use it and am not too familiar.
i would flash up to 1.04 just for increased media compatitiblity etc.
i think the issue with using PT with your Pioneer DVD-ROM stems for the fact that PT is programmed specifically for Plextor drives.
sounds like you're smoothing out all the issues you were having, that's great!