New Backerboard in shower doesnt line up with old cement liner

Question

I'm replacing a shower in our new home, because the old tile had totally cracked and rotted through. I pulled the old drywall out and am planning to replace it with backerboard. The floor is tile over cement pad, and I didn't pull the cement out (wood looked good both from in the wall and below). My plan was just to lay another layer of tile over the existing floor. For the walls we're just going to lay in big Formica panels. The shower is a tiny phone booth.

Here's the issue-- the top vertical edge of the cement pad is really uneven, and setting the backerboard on top of it leaves big gaps in some places. In a couple of spots, the raised tile will go above the level of the cement, so there will be a gap between the tile and the frame. Do I worry about those gaps? With the big panels of formica, there's plenty to anchor to. The plastic membrane is mostly intact, and I can patch the couple of rips that are exposed. If I am worried about those gaps, can I fill them in with something easily?

Thanks!

Pic. 1: Cement pad on right extends 1 to 2 inches above surface of tile. Pad on left is below level of tile, creating gap between tile and wall.

Pic. 2: Shows 3-inch section where cement pad has deteriorated and is now below level of tile.

Answer 1

My best recommendation is to rip out the existing shower floor and the old cement liner and start anew. Then you can rebuild this small "phone booth" sized space to properly work with the new sides and where they join the base. It may be that the use of a cement liner can be completely replaced with a newer technology. After all, if parts of the existing cement liner have basically degraded back to literal sand how sure can you be that that will not continue and have to be replaced in a few more years anyway.