Rod,
Certainly digital transport makes a significant different. Even the digital cable behaves rather differently when you throw in different transport and preamp into the mix.
I haven't heard the pioneer mod so I really can't say much about it. But a US$300 squeezebox can be modded to be a very good transport. Because hard drive playback get rid of jitters introduced at the CD rotating/reading stage.
If you want a state of the art transport, then I would suggest a Modified Northstar transport from Aberdeen Component, it's only US$2500 but it can more than hold its own against some of the mega-expensive transports like Wadia, Esoteric.
Rgds
barry