I think more of what he is asking is programs like sendg http://wiki.ultimaker.com/SendG
or another favorite pronterface
https://github.com/kliment/Printrun
The bottom line again is that the firmware is a gcode interpreter, so you send it commands via serial connection or read from an SD card.
You will have to configure those programs to the baud rates used by Makerbot firmware if using gen4 hardware, and then also know that because there was a change in the protocols, firmware MUST be before version 3.0 to talk at all. Right now, these alternate interfaces are more geared at gen3 or RAMPS firmwares, but I think they still will talk to gen4 pre 3.0 firmwares as well.
Good luck, you're going into unsupported land.
Also, don't forget that rep-G has a control panel where you can jog and control the bot for most normal purposes. I cannot really imagine your reasoning for manual control without greater explanation.
Also, if you were looking to print manually-it's been done before http://www.makerbot.com/blog/2011/04/18/gestural-3d-printing-printing-freehand/
I'm sure you could gather information on the interface that converted the sensory inputs to direct gcode for the printer.
