It's almost never a good idea to have any window in a wet area like you have.
Grout is not used in inside corners, sanded silicone caulking is used.
Drywall of any type should never have been used as a backer for tile in a wet area.
Grout is not waterpoof. There should have been cement tile board, fiber taped seams filled with thin set, then coat the whole wall with Red Guard to water proof it before the tile went up. There's several other brands of backer for tile that would have given you a 100% water proof barrier before the tile went up. All of the grout also should also have been sealed with clear grout sealer.
I'd bet also that if you put a level on all those water catching ledges there's no sloop to them. There should have been 1/4" per foot so water will not just sit there until it finds a way into a flaw.
If I had this job in my own home I would gut it, reframe for a transome window, repair the rotted wood behind the walls, treat the wood with bleach or Boric acid and hot water, add a 6 mil. plactic vaper barrier, and add tile board.
If a customer asked be to just try and "fix" the bad spots I'd pass on the job, it was designed wrong in the first place and any repairs done will fail I feel.
Another cheap way to get natural light into a bathroom without the chance of wall damage is to add a solar tube.