well...1. yes they're just scent marking. I got used to it too lol.
2. ahh the claws, i never found clipping them to be an easy task. SO, i took some 2L pop bottles, cut both ends off, then lined the inside with very high grit (mild, smoothish) sandpaper. you can just tape or staple it in. My guys never cared to chew them, they found either the sandpaper or the plastic bottle unpleasant. you can also have some not-smooth rocks (stones could be too small and get moved around) near the food and water. this helped my degus claws as well.
3. I hear ya. I had the SAME exact reactions, and it only seemed to happen as they got older. Keeping the cage as clean as possible helped me a TON. When I'd get itchy and hived up, a hot washcloth with a tad of soap was nice and soothing. I'd also have to change my clothes after, because there was dribbles that I'd later come in contact with, and the itchy hives would start all over again. Ask some folks about bathing the ratties. Not often, and you can make it fun for them. I bathed mine a few times, it helped, and even more so if I'd bathe them the same day I'd clean the cage. Nope, no cortisone cream or lotion ever helped me either. Just a warm wash would help me. Best wishes!
"If you can't change your fate, change your attitude." - Amy Tan