As to your first question, some people do
let the bees clean the frames and equipment and they do an excellent job. But you run a very big risk of creating a robbing frenzy. Other bees will stumble upon this buffet, not only the bees from that hive, and when the frames and equipment are clean and dry, the foreign bees will go looking in the nearby hive for more honey!
Second question: Three eights of an inch is typically called "bee space". This is the amount of space inside the hive that bees will leave for themselves to move around in. This is the reason for the need for such exacting measurments when you build your equipment. If you leave any more than three eights of an inch, the bees will fill the space with burr comb, any less and they will block it up with propolis.
Third question: If you use an uncapping knife ( this is a heated knife which when used at the proper temperature slices through wax comb like... well like a hot knife through butter ) you should not have a problem with gouging out large chunks. Look on the www.dadant.com
site and they should have pictures of this knife in use.