You can't and NFCU shouldn't look at this deal as paying a fair price for the vehicle with the negative equity. You are not out of the negative equity situation. Those incentives are part of the fair market value of the vehicle. The current fair market value is ~$23k for a 2WD XLT and ~$27 for a 4WD XLT.
Then start subtracting depreciation (~$9k year 1, then ~$2k per year after that) and you will see your future value. So, you can see how hard it is to create equity with a loan of $40k on a vehicle that will be worth sub $20k next year. This creates a cycle of more and more negative equity.
Stop the cycle by paying significantly more than the minimum payment on the vehicle. It would take roughly $1,500 per month to get into equity within a year.
From your post, it looks like you were buying a vehicle based on the monthly payment. A "low" monthly payment is your enemy on a car purchase. That just means you are getting into a much longer term than you should. A longer term (over 60 month's) generally carries a higher interest rate. To "save" a bit each month, you are wasting thousands of dollars on interest charges.
Get this loan paid down to match the market value of the vehicle, then refi into a short term-low rate loan.
Congrats on the new vehicle and best wishes to you in getting it paid down.