Clutch gives a ground signal, brake does a +12v signal. Simple relay crap should work.
If the clutch switch is the only difference, all you need to do is wire up a low-power relay between the clutch and the controller's brake input. +12v to the coil, clutch switch to the other coil wire, a diode upstream on the clutch wire, then wire the +12v to one NO pin, and the controller's brake input to the other NO pin. Add a diode (actually a few in parallel) between the brake switch and where your relay intercepts that wire. If you do the diodes correct, your clutch should not turn your brake lights on.
Otherwise, remember to use the brake instead. I did an auto-manual on an EF, and until I naggered a wire into the system, it would slowly rev if I hit the clutch to take out of gear. ;D