I'm not a pro, but if I was doing it, I'd replace the whole thing. With the flooring and sub flooring already up, this shouldn't be too difficult or expensive to do. I trust you know the flange is supposed to set on top of the finishedfloor, be screwed through both the finished flooring and the sub floor. Do I read your question correctly that you are looking for a 3" flange that fits inside the drain pipe? These are not recommended for 3" pipes as they cut the inside diameter of the drain too much. I've never used ceramic tile personally, but those who have recommend dealing with the holes for the screws when laying the tile rather that drilling them afterward. They don't have to be pretty or sized perfectly. I'd use #12 stainless steel screws to anchor the flange because they are stronger and less likely to break than brass. Don't cut the pipe and fit the flange until the flooring is all down. That way the flange will be firmly on top of the floor.