I am confused. You ordered new one for 3999, but the new ones are in the 5K range. What model year did you order?
To try and answer your question. 2014 Core models are not 1000k cheaper. The price change from 14' to 15' is maybe a hundred bucks. The price difference you are seeing is likely Artist Package MAP price or the MAP 10 top price. Either of which, regardless of year, is going to be a little higher obviously than the Core base MAP price. I think you maybe seeing Artist Package MAP prices, which is going to be just over a "G" higher than the Core line. A Maple or Rosewood neck will bump it up a little higher still.