How high should I mount the nesting boxes? Or do I leave them on the floor?
My method for determining height.
Determine the height of the coop floor, including bedding.
Design your pop door so the bedding does not fall out. Human or cleanout doors also. The chickens will scratch the bedding so they should be raised a bit.
Install your nests. Some people put the nests on the floor. Some like them high enough so they don't have to bend over to gather eggs or clean the nests. Some stack them in different rows at different heights. People tend to care much more about nest height than the chickens do. Make them convenient for you.
Install your roosts higher than the nests or anything else you do not want the chickens to sleep in. Most chickens like to sleep in the highest spot available. You don't want them sleeping in your nests as they poop where they sleep. I find it very convenient to catch a chicken on the roost at night if I want to catch one instead of chasing it with a fishing net during the day. That might be to inspect of treat one. So make them a convenient height for you to grab a sleeping chicken.
I want my ventilation higher than the chickens' heads on the roost. You don't want a strong cold wind hitting them in the winter. If the ventilation is higher than the roosts that isn't a problem.
And Poop boards under the roost. What's a good way to make those and clean them?
People do that many different ways. My 3' x 6' brooder is under the main roosts with a top that is a sheet of plywood. I scrape it off with a garden hoe that has a broken handle. My juvenile roosts are over my nests so again a flat sheet of plywood. I put the raked poop in my compost pile.
Some people build trays to hold PDZ or sand and scoop the poop out of that like you scoop kitty litter.
Some hang cloth hammocks under the roosts so they can take them down to shake them out. I don't see this one mentioned much.
People use other ways also. Lots of different options.