No harm to slightly overfill a manual transmission. If anything, it's more oil to help dissipate heat better.

Amsoil Synchromesh did wonders for my Cruze's 6-speed transmission. Give it a few shifts and it loosens right up even when stone-cold.

It never ceases to amaze me what junk fluids the OEM's put into their manual cars, at least the cheaper ones.
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2009 Honda Fit Sport
2012 Chevrolet Cruze Eco