If you are using the jog wheel to scroll through ticks in a sequence, it will send the appropriate midi commands to control the position pointer in a DAW, and of course STOP START CONTINUE work if you are sending clock sync. These are hard-coded messages that cannot be altered by the user from the MPC..
Of course the pads can be configured to send any note within the MPCs (still limited) note range. Also, if the latest version of the MPC 1000 JJ OS is used, you are able to configure the q link faders to send controller messages via midi.
That's pretty much it, there's no "alternate controller mode" and none of the other controls have any capability to send midi signals.