Oh man this is just really sad
I believe what you are saying and I really do think that you have this puppy. What is going on is just not a proper way to treat or train any puppy. It is not even reasonable to think that a 3, 4 or even 5 month old puppy would be house trained or even left alone for this amount of time.
You have so many issues going on with your situation that it is really hard to even break it down to just one thing. I am taking a guess that you are in your early 20's going to school,working a PT job and thought that it would be easy to have a cute little Yorkie puppy. Now it has turned into much more than you anticipated.
There is no quick or easy answer to what is going on with you or Scoody. My suggestion would be to try to rehome your little guy because I can tell that there is no way that you are going to be able to get his training and behavior under control. Sometime the most mature and adult action is to step up and take responsibility for a mistake and take appropriate actions to correct your mistake before you continue on a path of psycological destruction of the baby .