Why is the toilet backing up and bubbling after replacing an ejector pump

There is a clog downstream from both of these drains. If they are both at the lowest level of the house and you have a septic system, then it's conceivable that the problem is there, but you'd also see water backing up into that bathroom when you run any other showers/toilets in the house.

Most likely, the clog is in the joint in the drain lines where the shower and toilet join on their way out of the bathroom. Get a snake to fish down the drain (probably best to do this in the shower to avoid damaging the toilet bowl) and expect to go down quite a few feet before you reach the problem.

Edit: Revisiting this question, I'd agree that there's also a likely vent blockage from the bubbling descriptions. But the fact that toilet water backs up into the shower points to a drain blockage, too, and that will be easier to fix.

I'd start by snaking the shower drain. Liquid drain cleaners help with grease and oil buildup in the trap, but less so on hair or other solids, especially if they are further down the line (e.g. near the vent). The shower drain will be a lot easier to snake since you don't have to worry about damaging the toilet's porcelain finish.