The Extruder controller on my MakerBot has been erratic lately by shutting down during prints. I read on the MakerBot wiki (http://wiki.makerbot.com/cchb1) for the Heated Build Platform, that getting air flowing over the Extruder controller pcb will almost always keep it from shutting down.
I designed a low profile enclosure that mounts a 40mm by 40mm 12VDC sleeve bearing fan at the side of the Extruder pcb. This side mount design provides reasonable air flow over the board while maintaining access to the reset button and terminals which are not easily accessible with a top mount design.
I have uploaded the STL, G-code and SolidWorks assembly (.zip) files. With the uploaded G-code files, the total build time is approximately 47mins (24 mins for the funnel and 23mins for the fcover).

The assembly comprises of two parts to be printed on a 3D printer, four M3 nuts and four M3 by 25mm bolts.
Print the 3D parts, assemble and mount on top the controller pcb as shown in the photos. You can then run the fan wires to the fan pins on the controller board or run them directly to a 12V supply line (yellow & black wires) on the power supply.

Note: Remove the standoff nuts directly below the extruder pcb. This will provide sufficient clearance to fasten the fan mount.