you dont do anything to the flappers and i personally wouldnt touch the bottom dont see any real reason to i would say just use a dremal to smooth down the edges of the holes and and cut the walls off the top then sand it smooth and if u dont have a dremal they arnt to expensive to buy pluse if u do a kegger mod you will use it again or just barrow a friends if they have one
if you have any questions feel free to ask me and if i dont know the awnser ik someone who does
also if you do it urself dont rush it just take your time and keep a study hand