Good call on moving swapping the bedroom and the theater, and for finding the wasted space in the soffit. They are typically not built to conserve space and minimize their "footprint. The layout for the theater and the rest of the rooms is getting better with every revision. Tedd's last revision is really honing in on something good. Moving the door back from the front wall is a good idea and it helps with layout of the other rooms. The entrance to the bathroom at the bottom of the diagram forces a lot of unused space below the bathroom. Consider moving the bathroom door to the side and you could either increase the bathroom size toward the bottom of the diagram or use the space for something else, like a large storage closet.
You may be able to make the soffit going across the room near the front into an architectural feature, like a theater proscenium. I found the example below with a quick image search. It doesn't hide a soffit, but it does show an example of what a proscenium in a home theater can look like.\
Like from this thread https://www.avsforum.com/forum/19-de...struction.html
To address some of your questions and concerns:
If you build your walls so that they decoupled from the foundation walls, you don't need to use clips and channel, since they will already be isolated. It would be a good idea to use IB-3 clips or similar on the top to decouple them from the joists and the rest of the structure. This may require some rework, possibly taking down the walls and rebuilding them, but the material cost should be minimal and it would save you a lot on clips and channel. For the side wall that is not next to a foundation wall, you could either build a double wall, with the inside one decoupled from the rest of the structure, or use clips and channel.
For your ceilings, give strong consideration to installing drywall at the top of the existing joist cavities as shown in option 3. http://www.soundproofingcompany.com/...oof-a-ceiling/
It is a relatively easy DIY job that requires little skill, just time and patience. It usually involves grinding down staples and screws that protrude through from the floor above. The cost of the drywall and Green Glue isn't insignificant, but it will be small in comparison to the rest of the project. It provides a lot of additional mass that will help significantly with sound isolation. Once you move past this stage it will be near impossible to go back and add it later.
For any ducts that cross over the space to feed other rooms, leaving the metal ducts in place isn't a big problem. For any ducts that feed into the room, replacing them with flexible ducts is definitely recommended to minimize noise into the room. If there are any ducts feeding other rooms that are close to the ducts feeding the theater, do whatever you can to increase the length and replace any metal sections with flexible duct to minimize transfer between the rooms.
You should have a return vent. For every cubic foot of air that enters the room, there has to be a way to get a cubic foot of air out of the room. Most rooms are built to be rather "leaky" and the return is usually a big gap under the door. For a well sealed theater room, it is essential to have a return. My first thought would be to figure out where the return for the rest of the house is and try to tie into that. It normally feeds into the bottom of the furnace, usually from a duct at the side or the back. From there, it usually runs up and across the ceiling. It may be in the soffit at the middle of the house, or it may be in the soffit at the bottom of the diagram. If you tie into the primary return, use flexible duct with a lot of length to minimize noise transfer. The air going through from the rest of the house tends to be pretty fast moving and loud.
There are lots of options for sound treatments behind the screen. Here is a link to lots of them. Linacoustic is probably one of the most popular options. I lot will depend on what you can get from your local supplier.
Having a couple of dedicated circuits in the room is always a good idea. Two outlet that are added and installed together will not create a ground loop, as long as you stick with them for all of the theater equipment, including the projector. This excludes the lights, which should be on a totally separate circuit. A ground loop is commonly created when you use two different circuits (frequently an existing one and a new one) and you connect equipment to both circuits. All circuits have some resistance. The problem comes when you use two different circuits and one of them has more resistance to ground than the other. Two new circuits that are installed at the same time should have the same ground path and should have minimal to no difference in ground potential, resulting in no ground loop.