It still kills me that copper is considered the cadillac for pans in MA. I grew up in, and have worked in MA, so I'm plenty familiar with their methods. Some are so restrictive, some so lax, some so contradictory in nature. It still comes down to the pan being flat, and any imperfections in the flatness can lead to birdbaths (ponding), especially in the folded corners of the pan. While others will likely disagree, it's a failed installation in my world. The irony is that the installation is legal, and while the worksmanship, materials, and methods can be impeccable, a mud bed that retains moisture can be problematic over time. Some installations do need time to settle in. But if Bill recommended the guy, I figure your installer will give you a better analysis of what is occurring since he can put his eyes on the job, and he knows exactly how the floor and walls are detailed. I'm in Thailand now and your photos aren't loading. Probably not an issue with your photos, but with my internet connection.

oh geez, that is ugly. Total installer error. A sealer of does help reduce the chance of grout building up in the cracks and crevices of natural stone, but by no means does it eliminate it. The use of a small brush, even something as simple as a toothbrush, during grout cleanup would have eliminated your problem. The solutions have been covered by Bill. Due to the thickness of grout that needs to be removed, this needs to be a combination of chemical (acid) and mechanical, with the mechanical "assisting" the acid. In overly simplistic terms, the acid will dissolve the binder in the grout, leaving you with the sand filler, that will simply fall away. Mechanical abrasion (a stiff brush to start with) will assist the acid in dissolving the grout and cleaning the tough stuff out of the micro-grooves and pores. If they show up with a jug of muriatic acid, send them home. If they say "what's sulfamic acid" send them home. The discoloration on the grout after their premature cleaning attempt? That's why the instructions say to not use it on green (uncured) grout. There's usually a 10-14 day waiting period. Cleaners can get into the uncured grout and "burn" the grout, resulting in an unremoveable powdery-looking residue on the grout surface. You have so much buildup on the stone that I would not let them do a "mop" type of application, sloshing it everywhere. They need to apply it to just the built-up parts, because it's going to take several applications to get through the full thickness of some of those build-ups. If you have them proceed with the cleanup, find out what product they intend to use, then read up on that product before they show up to use it. Oh, and one of the beauties of sulfamic versus muriatic is that they could use muriatic that's so strong they could do more damage than good. With sulfamic, you mix crystals into cool water. Once you get a saturated solution, no more crystals will dissolve, they'll just sink to the bottom of the bucket. Don't let them mix sulfamic in hot water. That's a way to boost the amount that's dissolved and thus boost the "strength" of the acid. They need patience and multiple acid applications with this cleanup, this is not a one-shot attempt.

Yes. Polyblend makes something called Grout Renew that you can use to do this. They have it at Home Depot in a bunch of colors. I've bought it to take my white grout to grey in a bathroom, but just haven't gotten around to doing it yet.

If you didn't have the right materials then it really isn't their fault for using what you bought. However I would still get it fixed now. It will be easier than when it is finished. The grout saws get regular grout out pretty easily. Not sure about this type of grout. We used a premixed grout like this to regrout some floors and areas over door thresholds where our grout had cracked. It was harder than normal grout but also more flexible so has not recracked over the thresholds. But we did not use the grout you are using so I can't say for yours. Ours was not epoxy. If you have to eat the cost of the shower pan and some additional hours for the redo I would do that rather than end up with problems with the final installation. We did use a silicon based caulk to seal between our shower pan and a concrete shower. It has held up really well. The type we used was an outdoor window caulk because it came in an aluminum color. I have never had a regular bath caulk work as well as this one. We have a tub that needs to be recaulked and I think we will go with a outdoor window caulk again because the regular bath caulk seems to need to be replaced fairly often.