First off, get a wax ring without the horn...they are more trouble than they are worth. If you moved the toilet any way but straight down after compressing the wax ring, you probably created the leak...wax doesn't have any spring to it, and it won't bounce back. All you really need to do with the old wax is scrape it off...no need to make it like new.
A picture would help to see what the flange looks like. If the flange is sturdy and can't move around, and will hold the closet bolts, it should be okay. If the flange is too low (should be on top of the finished floor and be anchored through it - no space beneath it; i.e., flat on the floor), you may want to use flange extenders or reset the flange to where it is supposed to be. If it is too high, you may never get a good seal.