MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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The settings are:
// drive gear
drive_gear_outer_radius = 12.50 / 2;
drive_gear_hobbed_radius = 11 / 2;
drive_gear_hobbed_offset = 3.2;
drive_gear_length = 13;
drive_gear_tooth_depth = 0.2;
// filament
filament_diameter = 3.00;

The bigger MK7 pushed the filament guide more to right, so the idler is more smaller.
The 4th hole is now covered, you cannot put something inside...
When enabled for v2:
translate([20, 0, 0])
there is strange effect on generated item.
And i see only 1 half part, but there is no another half. It looks incomplete.
See image: http://imgur.com/909epAA

I re-design your extruder again to solve the problems. I will post it later when ready.
You have right MK7 might heavy for 3mm pushing. But someone reported it you need 2A version with high torque. It can generate 3KG push weight, and it worked.