Interesting question! What do you mean by "clean?" If it is an organic garden, as long as you did not use any chemicals what is there to clean? These are several schools of thought about tilling the soil as some feel it adds weeds to the soil. Another way to add nutrients back into out of growing season soil, is to plant a cover crop of rye or clover.
That's a completely different story. See if anyone is willing to clue you in on exactly where and how bad. Rats and mice are common in "organic" farm areas and since no chemicals or pesticides are used, it's an open buffet for them. Unless you have natural preditors to keep them in check, time to think about organic pest control. Contact your local Ag Extension or chat with Master Gardeners to see what might work best in your area. As long as you are not a commercial grower where policies and procedures are highly regulated in order to maintain standards, your cat or dog might be a good mouser. I have 6 rescue cats. So grateful they were rescued, they are the laziest cats on the planet. My Doberman terrier mix, however, is like a bloodhound, and will hunt them down for me. I just relocate them as I live on the edge of civilization and have a place to release them back in the wild.
Simple practices I used to keep my soil pest free can be found here.