Except that mice will almost-certainly get into them, and a 4-5 wk supply of food can be gone in less than a week. Seriously.
For protecton, i am fencing the entire area including the top and I plan to free range only after i know that all the birds return home and i know they are safe. I have those electronic eyes to install, Barking dog sensors at night, and i can install a webcam to watch the inside and outside of the coop. Yes - this will be an expensive project, but i don't want ticks on my kids.
A seriously-built run fence with well-installed electric that happens not to fail at the wrong time could "mostly" keep out foxes and coyotes and stray dogs and bears.
However you cannot fence weasels out of a large run, and weasels are very definitely in that area. They aren't much of a daytime problem but they will wreak havoc someday unless you can ensure all your birds are indoors at night behind a locked door, which means not just a reliable auto-opener but ALSO a regular training program for a good while (esp for guineas!). The guineas will want to stay outdoors at night. If they roost in a tree that cannot be accessed by raccoons (from the ground nor from adjacent unprotected trees) this is ok BUT to keep them from flying away you would need to have the run top that you speak of be ABOVE the branches where they're roosting.
A large run top will come down in the snow and is unworkable for a yard-sized run in a Catskills winter.
You also cannot fence out rodents that will steal food. You WILL have them.
If you put in electric fencing and it happens not to fail at the wrong time you could "mostly" keep out raccoons as long as there are no trees outside the run that overhang the run or hang close to treebranches from inside the run.... otherwise, raccoons will get in.
Also,
all electric fences fail sometimes, usually at the worst moments, and if you are gone for 3 wks at a time there is a pretty decent chance that you will have bear/coon/coyote type losses.
So how do i keep the coop clean
Sorry, but I think that is irrelevant because I do not see any plausible solutions to the bigger problem of "how do I keep the birds alive".
I really am sorry, I hate to be a wet blanket to all your fun plans, but you just cannot keep poultry safe on an every-3-wks basis. If you were going to hire someone really dependable to check on them a couple-few times a week, then I'd say well maybe you could make it work with a certain amount of luck.... but WEEKS on end? No.
An occasional cottage is just going to have ticks around, it comes down to whether you're ok with that or not.
Best of luck,
Pat