I'm going to use aluminum L channel to keep it all together and a rubber membrane to block water.

Cut around the brackets, then fill in and level with a floor patching compound.Or I'd do a tile floor with an isolation membrane -- I don't like that crack in the corner much, either.

After a bit of research online, it seems that the problem stems from the contractor’s choice of using pre-mixed mortar to affix large format tiles over Ditra, a waterproof membrane.

Basement waterproofing can cost few thousand dollars for the french drain, the sump pump installation and the drainage membrane.

Older stucco was solid but not built with a waterproof membrane, so water gets behind it and then just rots everything out.

I'd go in to do finish work and find major flaws, like walls ridiculously out of square, grout over-watered to spread easily and setting up soft, or the flat surfaces of a shower window and niche not pitched properly nor the CBU sealed with a membrane.

In a small house, i would drop USG Tile Membrane and tile it, small easy and mice upgrade. here is a link to the membrane, no duraroc needed. https://www.usg.com/content/usgcom/en/products-solutions/products/performance-flooring/ancillary/usg-durlock-tile-membrane.html

Also apply the paint on rubber membrane before putting any tile or coriander.

There should be some type of valley flashing whether its metal or rubber membrane between the roof and the wall. 

Vinyl and hardi will allow your flashing membrane to turn up the wall.