I would double check the paws - they get dry and cracked this time of the year. Just a little crack or scratch is all it takes for the blood spots. As for how to prevent this (if it is a paw dryness issue), bag balm is a popular remedy.
The other medication that you're thinking of is Reglan. The Baytril is probably what is causing Jack not to eat on his own, and therefore not pooping much. Try to feed as much as you can. You can also see if he will eat some alfalfa hay - especially the leafy part.
Peroxide is good for cleaning pee off of wood. Sanding helps too.
If they keep peeing and find that they ruin wood shelves, consider tile shelves. You cut a piece of ceramic tile to the same size as the wood and glue them together with Elmer's Wood Glue Max (it's waterproof). Keep in mind...
The thing that I found to work best is to add bleach, use hot water, and 2nd rinse. I wash 6 liners at a time and put in 4oz (1/2 cup) of bleach after the machine fills up with water.
The only thing Superpet makes that I buy is their glass water bottles. A lot of people don't even like them because of leaking or lack of water, but I have never had a problem with them as long as I shake them after filling them up.
But yeah, other than that, their products are garbage.
You can get a metal pan from here:
http://www.bassequipment.com/Cages/Ferret+Pans/default.aspx
Plywood might work short-term as long as the chin couldn't chew it, but I imagine it would get nasty from being pee'd on.
Critical Care is a food replacement for animals that aren't eating on their own that you syringe feed or some chins will eat it off of a spoon. You should be able to get it at a vets office, you might have to call around. Baytril is known to make chinchillas loose their appetite.