You are right. You cannot jog the machine while g-code is paused. This has come up a few times. I don't know How much of a change to emc2 that would require to make possible.
The only thing I can propose is using the tool table and a tool setting switch. You would only have to set the first tool.. Then the rest would be set by the switch.
this is a gcode sample.
http://cvs.linuxcnc.org/cgi-bin/cvsw...e=text%2Fplain
sam