I can't leave it at that. Here is a new fan for the heat-sink. The original hardware should just work for these. It might be a close fit for you if you find any extra screw length.
Here is my fixed version.
The holes were 1mm too far apart in 1 direction so I brought them closer together. I also added 1.5mm to the base so that I could get the screws out of the heat-sink area. It looked like they were going to interfere. I assume, that is why the dimensions were off to begin with.
This was edited from the original STL so my sketchup model is hard to edit but feel free to try. This took an hour to clean up before I could even alter it.
EDIT: Just tested it out. It works great! The stock screws should be perfect
Post's attachmentsE3D-v41_Fan_Duct_2n2r5_fix.skp 159.91 kb, 20 downloads since 2013-07-15
FanDuctForV4.1_2n2r5_fix.stl 422.42 kb, 50 downloads since 2013-07-15
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SD3 w/ mods:
Glass bed with QU-BD heat pad upgrade, threadless ballscrew w/ 8mm smooth rod, spectra line belt replacement, lawsy MK5 extruder, Lawsy replacement carriage, E3D hotend, Ramps 1.4 w/ reprap discount controller, DRV8825 drivers, 12v 30A PS, Acrylic case, Overkill Y-idlers, Filament alarm, Extruder fan + more.