Your parts are not in the Prusa Mendel i2 as found here or here.
Also note, quote:
Parts included in Github repository have the wrong dimensions for the
nut traps! Download the correct version from [Thingiverse Greg's
Hinged Accesible Extruder]
Are you sure you have the correct parts for the original Prusa Mendel i2? Maybe you have a different version? The original extruder mount uses an M8 hobbed bolt, not an MK8 hobbed extruder gear. The first is 8 mm in diameter, the latter is 9 mm in diameter.
After you updated your post to hint to the correct printer, it appears that my answer still holds. You did use the incorrect extruder gear. The 9 mm gear doesn't fit in the extruder part as it requires an 8 mm diameter extruder gear.
It might be difficult to find a 8 mm hobbed gear with a 3 mm shaft diameter, they are usually 5 mm (as in the stepper shaft diameter) or 8 mm (as in the diameter of 8 mm bolts that are frequently used for extruder setups). You could redesign the part (load STL in a 3D CAD program and make the changes). By the way, PLA should not shrink so much. As can be seen in the photo's, it looks like your current printer does not print very accurately, that may also contribute.