It's true, it can be a pain to change some things. Have you checked into a special order walk-in yet? I used an off the shelf sink in my small bath and replaced the vanity in the master bath. Had drain line issues in both baths but for different reasons. With the improvements you've already done I'm sure you can work this out. What you've shown us so far looks great!

We redid our MB with an overhead, a hand held, also a grab bar. I think the handheld is great. We use it for cleaning screen windows, the dog, sometimes my feet, etc. Although I think the ceiling overhead shower head looks glamorous , it makes washing your hair awkward. You have to step out of the water pathway to get the shampoo in your hair, vs. a wall mount you step back a few inches and you can get shampoo in while still being showered with the water.

A good quality manufactured shower base/receptor can be very nice. Kohler make some nice ones from acrylic and some from cast iron, I think the reason people don't usually like them is that they've stood on ones that flex....cast iron won't do that. Then there is stuff like Corian that is sold through dealers. They make the floor installation a lot easier, but you obviously have to like the way they look. But it is far more sensible to use a continuous waterproof tray made in a factory that you just put down rather than assembling layers of plastic, mortar, waterproof membranes and finally tile and grout that is not waterproof. I very nearly used a Kohler base, but they didn't make a large enough one in cast iron and so I would have had to get a custom solid surface one and it was just easier and faster to put down a mud floor and waterproof it and tile. I think your contractor should remove the existing floor as who knows what's going on with the liner or maybe install something like the Kerdi system that you tehn tile over. They have a system that makes a lot of the tricky aspects of shower construction quite simple.

The only way to get help here is to post a to scale floor plan . IMO free standing tubs are a PITA to get in and out of and IMO will be as dated as the corner tub you have now very soon.So post the floor plan and also some info as to what can be moved as far as plumbing is concerend. Keep in mind moving a toilet is expensive but can be done. Free standing tubs need lots of space to look right BTW