I use my 4000 either by sampling direct into the unit and/or by sending wav's via aksys as recorded in Pro Tools via the 192 interface (often from vinyl). I don't really distinguish a major difference between output from the 4000 samples and direct aksys'ed wav's from the DAW when using samples from a source like vinyl.... The 4000 sounds great, but for me its more about how it works as an instrument when you use it with the onboard sequencer, this is probably the most important point. Depending on the music you're making you still can't (for me) get that instant vibe from programming on the computer based sequencer as opposed to hitting the pads and seeing what happens. . .
I'd check the www.mpc-forums.com
for very specific info for this unit, often the discussion there is not quite so pro as on Gearslutz but you may get more info. An alternative maybe to use the ADAT option to go direct and bypass any A/D to the DAW if thats a problem but often its what you put after the analogue output that helps give it a little extra. .... If i've got your question wrong, apologies..