A bunch of gys on here have done this mod, and I don't recall anyone discussing manual transmission cooling as a problem. Search for bellypan projects and PM someone. I think the aerocivic has had a full pan for close to a decade. When you say you left an opening, what kind of opening? It is likely to scoop airflow or just vent it out? Is any part of the front grill open, so that air is getting into the bay under higher pressure and seeking a way out?
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See my car's mod & maintenance thread and my electric bicycle's thread for ongoing projects. I will rebuild Black and Green over decades as parts die, until it becomes a different car of roughly the same shape and color. My minimum fuel economy goal is 55 mpg while averaging posted speed limits. I generally top 60 mpg. See also my Honda manual transmission specs thread.
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