For the bathroom floor use thinset spread with a 1/4" notched trowel as your "glue", then screw. In the shower, no cement board under your shower pan. You can use a preformed shower pan, 36" square is a very common size. Do a google search for "36" shower pan" and you should get quite a few hits. They come in different types of plastic, in Swanstone material, there might be a cast iron one out there too but I think Kohler's cast iron receptor is 36" by 48". If you want to build your own, Harry Dunbar has a nice pictorial showing how to do it with a conventional membrane here. There are also tole bases made by companies like Schluter. Noble, Wedi, etc, but they are shower "systems." You use their material for the base and walls. Here's a lengthy thread with lots of photos a DIY deck mud preslope covered with Kerdi, as well as a complete Kerdi shower. There are myriad ways to skin this cat. Mongo

"So he built the sloped mudpan, coated it with Hydroban and installed the bonded flange drain with specified 1 1/4" height from the substrate and then when he went to install the tile he said that in order to get the tile height to what Laticrete specifies it should be (1/16" higher than the top of the drain) he had to build up the mortar and basically try and follow the slope with 1-2" of mortar. " If that's how he installed it, he completely misunderstood the installation instructions of the drain. The drain flange gets installed so the rim of the flange is 1-1/4" above your FLAT PLYWOOD SUBFLOOR. Not 1-1/4" above the sloped mud bed. If that's what he did, it's completely wrong. Again, the drain flange should have been installed so the rim of the flange is 1-1/4" above the subfloor. That 1-1/4" gap between the flange and the subfloor then gets filled with deck mud, and the deck mud then slopes upwards as it runs from the drain to the walls so that it's 1-1/4" thick at the drain and, let's say, 1-3/4" thick at the walls. An increase of thickness of 1/4" per foot over the 2' distance to the wall. When the sloped mud bed is complete, the drain flange should be set perfectly flush in the deck mud. Then the mud and the walls get hit with two coats of HB. You then tile the floor but leave a few tiles out around the drain. The actual drain cover (the metal grid) is attached to a threaded plastic piece that gets threaded (or screwed) into the drain flange. You thread it down so the top of the drain will be at the approximate height of the top of the tile on the floor. In your case, for standard tile, about 1/4" above the flange. So the drain height is set in relation to the tiles already set on the floor. Then you complete the floor tile by filling in the remaining tiles around the drain. If the deck mud was properly sloped, all you'd need is the standard 1/8" thickness of thinset to bond the standard 3/16" to 1/4" thick tile to the sloped and Hydrobaned shower floor. The beauty of a topical membrane like Hydroban is that with the Hydroban membrane being right below the tile, there can be no deep wetting of the shower floor like with a traditional deck mud bed where the membrane is beneath a 1" to 2" thick layer of deck mud. Your guy put 1-2" of mortar or mud on top of your hydroban membrane. You have a porous tile (marble) on top of that mortar bed. That 1-2" setting bed will likely saturate over time. If the bed does saturate, the moisture can bring minerals from the setting bed with it through the marble and grout as the moisture evaporates, you can end up with efflorescence on your marble and/or grout. And with the bed holding moisture, it can end up being a mold/mildew mess. Those are not certainties, but they are possibilities. Also, if he used thinset to make up that 1-2" thick bed, that could also be the reason the floor has birdbaths. Thinset is designed for "THIN" tile setting applications. Roughly 1/2" thickness max of thinset. The reason is because as thinset cures, it can shrink. That shrinking could pull the tiles this way and that, causing birdbaths here and there. I don't mean to be an alarmist. But if I'm reading your post correctly, your installer screwed the pooch on your shower. If you haven't seen it before, watch this Laticrete video. There's a bit of an intro, but do pay attention to the installation of the drain flange at about 2:30 into the video, and the installation of the threaded drain at about 4:30 into the video. The Laticrete system is an excellent shower system. Sorry for you troubles.

A properly packed mud base won't shrink or change slope after it's packed. Proper analysis is as simple as taking a straight edge and give the pitch of the entire floor a good once-over, looking to see if it's a simple depression in that one area. A "bird bath" so to speak. If it's a simple bird bath, then the tiles in and around the area can be cut away, the mud base can be rebuilt, and tile reset. How few or how much of the floor tile needs to be pulled up is simply a factor of how much of the floor is improperly pitched. Going off the intersection of the floor tile to the wall tile and how the tile falls away from that area, it does indeed look like the slope peters out a little to early, though it's tough to tell off of 2-D photos and not by putting a 3-D eyeball on your shower floor. So as laz inferred, if it's tile over deck mud with a buried CPE membrane, the repair is fairly easy. If it's tile over a topical membrane, it's still repairable, but a bit more involved. Best, Mongo

If he gives you push back on rebuilding the whole shower, pull up your local plumbing codes. Our city's plumbing code says this: 417.5.2 Shower lining Floors under shower compartments, except where prefabricated receptors have been provided, shall be lined and made watertight utilizing materials complying with Sections 417.5.2.1 through 417.5.2.6. Such liners shall turn up on all sides not less than 2 inches (51 mm) above the finished threshold level. Liners shall be recessed and fastened to an approved backing as not to occupy the space required for wall covering, and shall not be nailed or perforated at any point less than 1 inch (25mm) above the finished threshold. Liners shall be pitched one-fourth unit vertical in 12 units horizontal (2-percent slope) and shall be sloped towards the fixture drains and be securely fastened to the waste outlet at the seepage entrance, making a water-tight joint between the liner and the outlet. The completed liner shall be tested in accordance with Section 312.0 417.5.2 Shower lining Now as far as the idea of only replacing the floor? I always read on this forum that it can't be done because it will no longer be waterproof. But I don't have the knowledge to type out the reasons why. Maybe a pro on here can give you the language to use with your contractor in case he gives you push back on that and continues to say he can just do the floor.