Is your sewer line backed up? Perhaps you should have someone snake it and see.

It shouldn't be but who knows! It flushes fine

The shower has a trap that needs to have water in it. If the water dries out then sewer gasses can get in the house. Likewise with the toilet. If the toilet has been removed then gas can get in the house.

Oh- and with the toilet, the fixture has the trap, so when you have the toilet removed sewer gases can come right up... so it's not a huge surprise to be smelling sewer odor with the toilet off. Another reason that you are getting the smell could be that something in your bathroom isn't properly vented and is forcing gases back up the other drains. You probably should have a plumber come take a look.

When you took the toilet out did you plug up the hole with something? I usually ball up a couple of plastic shopping bags so the smell and sewer gas doesn't come in the house.

Yes we put old rags in the drain. He thinks it might be the vent is clogged. That's our next step, check that then maybe a plumber if the issue isn't solved. So of it's a trap problem can we just replace those pipes and all is well?

The vent pipe might be clogged. In Mn when it was really cold, the vent up on the roof used to dome over with ice so I would have to go up and either pour hot water in or knock off the ice dome. Never had that happen anywhere else I lived. The city guys said it was caused by my house being up on a hill way above everyone else on the sewer line. Stunk up in the house and outside as well.

I would think it would work to just replace the trap and pipes and it would work if that was the problem but I am not an expert.