Sound like you're really getting into this. One thing I did when planning my latest coop was to simply Goggle chicken coop pictures and stole the ideas I liked best for my situation. (I start chicks in the spring, enjoy the fresh eggs in the summer, and butcher in the late fall due to our severe winters)
I would suggest you raise the whole coop off the ground, maybe make it a sheltered part of the run. I used this line of thinking for my coop and our cabin, if it's on the ground something will hide under it (skunk,mice,bugs,moisture), if it's raised and a chicken or dog can walk under it, critters are less likely to set up housekeeping.
The trench I don't understand. We either bury some of the wire to prevent digging under or let it come down to the ground and leave 12" to 18" on the ground around the outside to keep dogs, fox, etc from digging under. Also, depending on your run size, keep it narrow enough and tall enough to throw deer netting or fruit tree netting over it to keep out areial predators.
Soffets are up to you but be sure you have a lot of airflow as coops get hot and chicken poo fumes can get pretty intense for you and your birds. The vinyl flooring is popular and should not be a bug issue if you glue it down and set your walls on top of it. It also is easy to clean (see the thread about using sand on the floor)
Outside access egg boxes are real handy and you don't risk startling your birds and one getting hurt if it's dark when you collect
If you insulate the floor, remember to cover it on the underside as squirrels like to steal it and the chickens will peck at it, especially foam board, if the have access under the building. Also pitching the floor to the door helps when you do a major hose down cleaning
It's fun building your own coop as you can add your own personality and flair to it. Please post a photo as we would love to see it (maybe we'll steal one of you ideas for next time)