I've never taken keys off before, nor had to. I remove the membrane, lightly clean the whole of it with isopropyl alcohol (contact side obviously). As for the actual keyboard - I normally fill the sink with warm water, and lightly scrub at it with a dishwashing brush or something (firm long bristles) whilst applying washing up liquid to the brush as needed...and this removed all the dust and dirt from on and underneath and around the keys. The caps lock window and LED will be fine, so forget it's even there.
Rinse well under running water (both sides) and shake off excess water. This may take a few minutes to really shake off all that water (and requires effort). Then you can leave it to dry naturally. Once dry, get a clean cloth and clean those rubber pads if you feel it's necessary with WD-40. The isopropyl alcohol is just as affective but can turn some rubber brittle and make it crack (so I've heard, but this has never happened to me yet).
Option 2 is to put it in your dishwasher if you have one (I don't). You can find info on option 2 by a bit of googling. Personally I'd much rather strip-clean it manually, particularly in your case being as though you have slight problems with certain keys.