as far as how long to ozonate, as ozoneman said 10 to 20 minutes is fine. som ewill tell you that its pointless to ozonate for any longer than a half hour or so.
however, i have experimented with ozonating for longer periods and i truly believe that the water continues to absorb oxygen for a long time. the first 20 minutes or so i think it absorbs at a very high rate. after that the absorption rate falls, but my experience tells me it doesn't stop. i have drank ozonated water that i accidently left ozonating for 4 hours because i left the house. wow! that was an intense experience! you can't tell me that that is was the same as drinking water ozonated for 20 minutes!
but i mean for everyday use 20 minutes or so is just fine, don't get me wrong. you are getting lots of benefit. but i usually ozonate mine for longer. its not like you have to pay attention to it. you plop the stone in and then go about your business. i personally like to ozonate my everyday water for 30 minutes or so. then i do a glass for an hour or longer every once in a while.
breathing is a personal thing. you just have to experiment with the fumes. if they bother you just be sure to put the glass near an open window.