Clean water, preferably something that filters out Giardia if i remember correctly. I personally use a Pur filter. It just attaches to the end of a faucet. Glass water bottles are definitely preferable too, since a chin can chew through a plastic one.
Fresh Hay - they get as much hay as they want to eat generally. Oxbow is a good brand of hay, and the one i use. So far i haven't seen a pet store that didn't carry it. Hay not only provides nourishment that they need but it also helps wear down there teeth which they need to do. But an FYI; they are a bit picky. There is often hay left over that they wont touch. So expect that.
Pellets - Always a lot of talk and different opinions/preferences about these. Rough estimate for daily amount is about 2 tbls a chins. Some might go more and others less. Chins generally don't over eat so you don't have to worry about over feeding them. Many ppl don't even measure the food at all. I personally like too just so i can more easily notice if there is a change in the amount they are eating over time.
You want to avoid anything with supposed 'treats' in them. They are usually not healthy. Any fruit or veggie, anything with sugar content, or corn, you want to avoid.
Mazuri and oxbow are two popular brands to use. I have never used mazuri before but i think i remember hearing ppl talking about it causing diarrhea in some chins. Would need someone else to confirm that tho. I have used oxbow when my regular food was out of stock. I never had any issues with it, it was pretty good.
Some ppl like to use rabbit foods. But you have to be careful with that. Not all kinds are safe for chins. The kind i use myself is a rabbit food. Select Series Pro - a MannaPro brand. The down side is the only store i know of that has it is Tractor Supply (at-least around me.) The up side for me is that a 25lbs bag is like $7-9. Where as the oxbow and mazuri in a petsmart type store is something like $15-20 a pound.
--
Plastic is generally a no-no. Chins teeth constantly grow so they chew things up to grind them down. They also groom each other, and figure things out by chewing them. Kinda like how a baby puts everything in hes mouth. So if plastic gets ingested, naturally it can cause health problems.
Most ppl like to replace plastic shelves with cuts of chin safe wood. Take a slab and make there own shelves, or they can buy them from various vendors on here. It not only works as a shelf, but can double as a chew toy for them. Poplar and Kiln Dried Pine are the two types of wood i hear about most. But the only kind available around my area is poplar. So it will depend where you live if you want to make your own some time.
They could be freckles on his ears. There are many many variations of chinchilla colors and traits. Some of them do include freckles on the ears. Three of my five have them. If you can post a pic of the chin im sure someone can help you with want type of mutation the chin is (and whether or not the spots on the ears are natural.)
The feet of my chins are usually somewhat rough. They are on there feet all the time so it is not uncommon. As for any feet specific injuries/problems/sicknesses, or anything like that, that is not my area.
After all my years with a chin, i honestly cant tell you if a chins ears normally feel rough. None of my chins like having there ears messed with.