Thanks for the suggestion!
I hadn't thought of using 2x6's. Sounds like a good idea!
Just to make sure I'm not screwing this all up, I have attached more photos to better represent my situation.
In order to make the tub fit correctly, and keeping the room square, I figured that I would need to rip some 2x4's to just barely enclose the vent pipe.
But, the toilet rough in will be 12 inches on center from the studs, so I have to get a 10" toilet, right?
I also have a standard tub at the end of the bath. That rough in seems to be ok. As you can see, I have already dug it out and attached the drainpipe to make sure it fits. (I am really paranoid about screwing this up!)