new civic does not have a differential, it only has a transaxle,yes transaxle is a transmission and differential combine in one piece. you put the oil in the gearbox, theres a drain bolt below the gearbox open it oil drains out, then you use a manual pump to pump manual transmission fluid back though the same bolt.
valve clearance are the small gaps on top of the valve stems and th part which presses them to open. you dont need to have the tappet adjusted after 40k unless you face a rattling noise or have trouble starting etc, best not to mess with them. you cant even adjust the valve clreances in toyota's 1.6 2zr-fe engine anyway it requires shims.
if you ever go for valve adjustment make sure to do it with feeler gauges and according to ta values mentioned in the owners manual.