there is no better upgrade for this car than the acuity shifter, i cant say enough good things about this shifter. My fiancé even told me its the best upgrade I've done to much car to date! Yes I let my lady drive my Si whenever she wants to, I taught her how to drive stick in case I'm ever...
i chalk it up to the shifter just needing to be broken in, mine still does it occasionally after 33k miles. but for the most part its super smooth and only really happens when i down shift into 3rd gear.
mine was a 95 civic DX coupe with a 115k on it, had it through 6 deer hits and 75k, and sold it with half the bumper missing for $600. it lasted my buddy another 4 year till hid crashed it driving like a moron.
i tend to think teaching barefoot is easier for the new STICK driver to feel the clutch engagement point. when i taught my fiance i had her do it barefoot in my 2009 civic, she was driving on her own within a week.
id say you got bigger problems, that sounds awful. sounds like you need to dynamat your trunk to avoid further problems. i have a 12 inch sub in my trunk and have zero rattle anywhere. that's more of an earthquake than a rattle!