The DC motor used on the MK5 Extruder head seems unusually prone to sudden death, either by mechanical failure or something electrical. A stalled or shorted DC motor becomes a low resistance that destroys the A3977 H-bridge driver chip on the Extruder Controller board.
Makerbot recommends inserting a 10 Ω power resistor in series with the motor, so as to limit the maximum current. Other folks have build a diode decoded relay driver that’s certainly more durable than the A3977.
Downsides:
The power resistor reduces the voltage available to the motor, which draw something like 40 mA when unloaded and up to maybe 250 mA at full load. I don’t know what load the extruder puts on it, but at 100 mA the resistor drops 1 V, which seems excessive.
The relays seem like a nice solution, but they go clickety-clack and require actually building something, of which I’ve had quite enough lately, thank you very much.
While I was mooching those lugs, my buddy Eks suggested simply putting a low-wattage 12 V incandescent lamp in series with the motor. The cold filament has a very low resistance, but limits the current when if the motor shorts out.

A bit of rummaging in the Lamp Box produced an old automotive #89 lamp that allows 560 mA into a dead short, which works out to 7 W.
If the motor draws 100 mA, it drop only 100 mV: good enough!
Not finding a suitable socket in the heap, I wired it in by soldering the wires directly to the brass shell and central solder tip and taping up the mess. Next time I get near the local AutoZone I’ll pick up a socket.
The Anderson Powerpoles may look like overkill, but they make life a lot easier when you’re fiddling with the machinery all the time.
Now, the lamp won’t prevent inductive transients from blowing away those puny signal-level Zener diodes that should protect the A3977 chip, but it’s exactly what you need for long-term overload prevention.
[Update: An experiment that shows why a lamp works better than a fuse.]
As an added benefit, when the bulb lights up you know the Extruder Motor has died!
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