First, congratulations on putting your inheritance toward debt! Debt can be a psychological ball and chain. You are on your way to freedom.

Question 1: Do I prepay (A) or (D)? As a general rule, you want to pay the highest interest rate off first, regardless of the outstanding balance.  You will want to pay off (D) $3365, and then put the remaining $1635 toward (A).

Question 2: For this, I contacted Navient and the customer help said that you do the following:

1. First, make a monthly payment on the loan. Then in step 4 you can make payment on principle.
2. Go to the loan you will pay off (D) and find what the payoff amount is for the loan.
2. If you will pay online, select 4-day payoff (because that's how long it takes to settle). If you will send in a check, select 10-day payoff (takes longer by mail)
3. After you have made a monthly payment, you may go back in to make a second payment. The system will ask "Will this be a future payment?"
4. Answer "NO" because you are making a payment on principle.
5. Make the payment of the 4-day payoff amount.

6. For Loan (A) follow steps (4) & (5) then put the balance of your $5,000 toward Loan (A)

7. The loan company will credit your account within four days (if paid electronically) but it may take 30+ days for you to receive a notice in the mail that the loan is completely paid off. You might also receive a small check for over payment of interest. 

Keep up the great work!