1. What are the things that some people don't think about?
The Cost definitely. The time and patience it takes. It isn't just one + one and a litter of puppies. It takes YEARS of research.
2. What are all the costs associated with breeding an akc litter (registrations, tails, dew claws, shots, etc)
I myself haven't bred a litter yet although I am getting my foundation Fox Terrier in late 2012/early 2013, but I have talked to breeders that have set aside money for breeding. One person I know have a breeding disaster and spent $10,ooo on a C-Section for only 4/8 puppies to live. You have to think about that when breeding.
3. How often have you lost puppies/mothers?
Haven't bred yet so can't answer.
4. When I do purchase, would it be a good idea to find a breeder out of the area so that I could be sure she wasn't related to my boy?
Well, it is possible that there are breeders out of your area who still have dogs related to your boy. Depends on his pedigree. You have to get look into pedigrees and check yourself.
5. Is it possible to look at the sire and dam's pedigrees when I'm looking at pups to compare to my akc boy's pedigree to be absolutely certain that they aren't at all related? - like, would that be an ok thing to ask of the breeder?
Sure, take all the steps need. 
6. My AKC boy is about 4 lbs. If I were to purchase a girl that reached an adult weight of 5 to 7 lbs, that would be an acceptable match, correct?
Sure! One thing I should ask. How old is your boy? I remember you saying in 3 years you would like to breed and I wouldn't breed any yorkie over 6 years of age. Also has he been health tested? Will the female be health tested (also expensive), so I would make sure her parents were health tested as you might end up spending thousands of dollars for a dog that might not be healthy. Also are you conformation showing? I would suggest breeding your babies as pets, breeding is always for the betterment of the breed and not just to breed. There a millions of yorkies in shelters so remember 
Btw, NEVER register a dog with the CKC (Contenital Kennel Club), they would register my slipper if I paid money. Honestly they are a just a hoax kennel club. Never register with them, I once had someone tell me they "registered" their Guinea Pig with the CKC as a Sheltie to see if it was really a bogus kennel club and they did it 