Instead of blocking off the areas have you tried using an X-pen? It is a metal pen that is open on top and they have room to move around. Also, if he has a crate, put the crate in the x-pen along with food and water. We are gone about 10 hours a day for most of the week and General Lee stays in the pen in the kitchen. After fixing 2 holes in the wall and several floor boards he now stays in while we are gone. He does not wet or poop in the pen and as soon as we get home, he is taken outside to go.
With another fur baby I had when we moved from the only home she had known, I took her off and on to the new place before we actually moved in to get use to the smell. Right now lots of patience and love is in order. He is stressed, but also pushing who is in charge.
I think the pen is a good size for him and he will adjust.
Good luck
