I think a little more concrete will need to be tapped out around the two stacks. That may help determine what the (third?) pipe is.
The shower needs to be vented before it wyes into a main branch. The way it was done before was wrong. Newer toilets require better waste and vents then before, simply because the flush is now so much quicker.
Waste pipes from above can't be used as vents for downstairs fixtures either.
Typically, a shower should be vented within five feet of the 2" p-trap. The vent can be 1-1/2"