1. I've got a couple of areas in some of my cages where there's a bit of slack in the mesh. I haven't had any problems w/it. Just be sure there are no tiny openings for escape or valleys where a foot could get caught.
2. You can melt the rough ends of the zip ties w/a lighter.
3. I haven't used those plans, so I don't know how to do that tray. Mine are on legs/stilts and I have a liner on the floor underneath.