I am a remodeler, but usually leave major DWV plumbing changes to the pros. The toilet flange can be replaced and relocated at the same time for proper standoff. Easy to snap iron with the right tools. That would also solve the old rusted nipple problems. Sink should now be 1 1/2, while tub/shower should be 2". Old vents will likely not be OK as exist, upgrade to 1 1/2 if not already.
Those old houses are so much fun. I did a bathroom last year, plumbing was buried in 5-6" of concrete. I knew there was a dining room below, but thought I would never get to the bottom of that stuff.