How to raise attic floor for new plumbing?

What you are doing is the right idea. Just build a box , fasten it down to the existing floor and put a floor on it. It will work out fine. You can go around it with trim later.........Just remember what people do around that toilet...........so keep it sanitary if at all possible. Good luck , I've probably done that 10 times for people.......so just do it and you will be ok.