closet flanges

Okay, so decided to tackle a home bathroom remodel. Bathroom has ugly pink 1 inch tile and I tear it out. Find out the subfloor is rotted so I replace that. Problem is, I cut the new subfloor around the flange, not thinking that the flange might have to be bolted to something. I redo the tile...

So I purchased two toilets standard 12" Rough in with out measuring finished wall to center of sewage pipe. (Dumb mistake/Inexperienced) When I removed the old toilet I encountered 3 very unpleasant surprises: The distance from the finished wall to the center of the riser sewage pipe was 9" ...