You have a pretty coop!
Keep in mind that poop will not decompose in sand, it'll get hard and crusty and just stay there until you remove it. I know others who use sand and love it, but they scoop and sift daily. I prefer shavings and keep adding more occasionally. My birds spends much of the day outside the run, so I only change out the shavings once a year, and all the old bedding and poop goes in my compost bin. You can add sand to the compost, but not on its own... you need brown materials to balance and break down the nitrogen.
I used to feed layer pellets, but I've discovered it's a bit overrated. I prefer Flock Raiser now. It has a higher protein content and it's appropriate for all ages (including chicks) and genders. With this feed, OS is a must.
This is my feeder secured with a bungee, and containers for grit and oyster shell hung with s- hooks:
If you don't want to enter the run often to fill the feeder, you could always make one like this that holds the entire 50 lb bag:
directions: https://blog.mypetchicken.com/2015/10/05/diy-no-waste-feeder/
Chickens do not see well in the dark and usually won't move, this makes them easy to catch. They should be going to sleep with a full crop and wake in the morning empty, that's the healthiest digestive schedule.
My run is fully secure and I feel comfortable leaving the pop door always open, some people don't. Food and water is in the run. This allows me to sleep in or leave town for a day or so and the chickens can come and go as they please.
Whenever you move chickens to a new location, they have to learn that it's home. You might have to help them into a routine for several days (like lift them up on the roosts every night). Soon, they'll be doing it on their own. If you let them stay out in the run, they'll learn to stay out there. I just feel better when my birds are inside the coop. If you're worried about them not going inside the coop at dusk, then an automatic door would just lock them out.
How big is your run and coop?
I see 8 chicks in your avatar... do you plan to free range?
I have sand underneath my coop intended for a dust bath area, but my chickens prefer the dirt floor of the other parts of the run even though there's a shallow layer of pine shavings on top. Actually, their favorite dust bath is a flower pot that they scratched all the plants out while ranging in my yard, so I gave it to them and refill it with dirt occasionally.1. Thoughts on sand in the run? I'm in Georgia and it'll be a covered run.

Keep in mind that poop will not decompose in sand, it'll get hard and crusty and just stay there until you remove it. I know others who use sand and love it, but they scoop and sift daily. I prefer shavings and keep adding more occasionally. My birds spends much of the day outside the run, so I only change out the shavings once a year, and all the old bedding and poop goes in my compost bin. You can add sand to the compost, but not on its own... you need brown materials to balance and break down the nitrogen.
No. You can line the boxes with a dishpan or something else removable if you prefer, or even shelf liner in case an eggs breaks it'll be easier to clean. I use excelsior pads from amazon because they're softer and stay together better than straw or shavings, and each one last many months (also compostable).2. Are removeable nest boxes a must?

I only have a gutter, rain chain and a collection bucket with a drainage hose that leads water away from my coop to prevent roof runoff from seeping/flooding into the run. I would love to have a full collection system someday... here's a good video I found:3. Rain barrel
A separate container always available fee choice. Loose shells will just get lost and buried.4. Oyster shells - do you just sprinkle them around or do you have a feeder in the run with just shells?
I used to feed layer pellets, but I've discovered it's a bit overrated. I prefer Flock Raiser now. It has a higher protein content and it's appropriate for all ages (including chicks) and genders. With this feed, OS is a must.
Many PVC designs are great, but I don't see the point of not going in, it would be a good time to clean the run or coop or check on birds. Cutting an opening in hardware cloth seems like it would just make it easier for rats and any other critter to find, or create, a breech. I just wouldn't do it myself.5. Feeder - I think we are going to build a PVC feeder and stick the shoots through the hardware cloth to outside the coop so we can feed without going in - thoughts?
This is my feeder secured with a bungee, and containers for grit and oyster shell hung with s- hooks:

If you don't want to enter the run often to fill the feeder, you could always make one like this that holds the entire 50 lb bag:

directions: https://blog.mypetchicken.com/2015/10/05/diy-no-waste-feeder/
This could be nice near the roost area. Poop doesn't always fall straight down. Somehow chickens manage to projectile splatter droppings on the walls while they sleep...!?6. Linoleum on the walls of coop?
Are you unsure? Or do you watch them running around in the dark?8. I feel like my chicks are up at night.. in general, they definitely sleep MORE at night but they seem to still eat and move about plenty. My original plan was to leave food and water out in the run and just leave the coop door open but now I'm worried they will not go into the coop at night, is this a problem? I was told that at dusk they will go in the coop and at dawn, they will come out? Should I close them in?
Chickens do not see well in the dark and usually won't move, this makes them easy to catch. They should be going to sleep with a full crop and wake in the morning empty, that's the healthiest digestive schedule.
My run is fully secure and I feel comfortable leaving the pop door always open, some people don't. Food and water is in the run. This allows me to sleep in or leave town for a day or so and the chickens can come and go as they please.
Whenever you move chickens to a new location, they have to learn that it's home. You might have to help them into a routine for several days (like lift them up on the roosts every night). Soon, they'll be doing it on their own. If you let them stay out in the run, they'll learn to stay out there. I just feel better when my birds are inside the coop. If you're worried about them not going inside the coop at dusk, then an automatic door would just lock them out.
The poop tray under the roosts! This is by far the best solution I've come across to keep odors and ammonia fumes away. I fill my tray with ½" of Sweet PDZ (zeolites) granulated stall refresher, then just scoop it like cat litter. It's easy, clean and efficient and also does great in compost. Since chickens seem to do most of their pooping at night and are outside most of the day, this allows the bedding on the coop floor to stay relatively clean.9. Any other amazing tips that have saved your life or made things WAY easier?

How big is your run and coop?
I see 8 chicks in your avatar... do you plan to free range?