The only two fixes I know for over extrusion so far are lowering flow rate to feed rate ratio and increasing the filament diameter. Is there a better way to do this without compromising strength? If not, what are the pros and cons of changing these two parameters?

The parameters you must change are Inset/Infill width over Thickness for infill, and Carve/Edge width over height for perimeter. Flow rate or filament diameter are not the settings to be modified in your case.

http://fabmetheus.crsndoo.com/wiki/index.php/Skeinforge_Inset#Infill_Width_over_Thickness
http://fabmetheus.crsndoo.com/wiki/index.php/Skeinforge_Carve#Edge_Width_over_Height

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François

I rather fix over-extrusion in the firmware (fixing ESteps per mm) than in the slicer software.

Anyway if you need to update it when changing filament type, it might be better to use the "Filament packing density" setting (in the "Dimension" module/tab).
For instance I recently tried Laywoo(d) and the hobbed bolt seems to bite much more deeper in that than in regular PLA.

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Most of my technical comments should be correct, but is THIS one ?
Anyway, as a rule of thumb, always double check what people write.