"Does anyone see any problems with the layout of the rough in plumbing to this point?"
Where's the vent for the WC?
If it's behind the wall, then the 2" line branching off the 3" before the 1/4 bend is going to cause a wet vent situation.
Are you aware that the cuts made in the floor joist completely ruined it from a structural standpoint?
Does anyone know of alternative plumbing pieces or ideas other than raising the floor or putting the stool on a platform?
Try using a 3x4 PVC closet bent and a 4" spigot ring. The 3x4 bend has a shorter pattern then the 3" st 90 you're using. Otherwise, build up the floor.