Hey Jmascis, A few suggestions to try during the break in period that I have found helped with my NOS New Hartford purchases that had been in the cases and not played for a few years like your D40.
First I went back to the factory brand strings which in this case would be Daddario's. Something I found with the John Pearse Phosphor bronze and even the light sets is that they seem to feel tighter for a week or two especially on the high strings. If I were you I would go ahead and put a set of the Daddario EJ16's on it and they should feel "Looser" right off the bat, Not to mention when they break in they will feel even better.
You need to check your neck relief and you should do this after you have the strings on the guitar you want to keep on it. The reason I say this is that your guitar came from the factory with Daddario Medium gauge Coated Phosphor bronze strings which have approx. 25-30 pounds more overall tension on them when tuned to standard tuning than the set of lights you have on it now. This means if the previous owner didn't have the neck adjusted when they installed the lights on it that the neck relief is still set up for the tension of the mediums. With the lighter tension of the light gauge strings it allows your neck to have less pull from the strings which causes the headstock to flex further away from the body of the guitar. This reduces the relief in your neck causing the strings to feel a bit tighter, At least in my experience anyways. You have a dual action truss rod in that guitar so you can accurately adjust the neck in either direction but when you do make sure to make very small adjustments (No More than 1/8-1/4 turn at a time on the truss rod) and then let the guitar sit for a few minutes before checking the relief again. Make sure the guitar is tuned to standard tension before you make any truss rod adjustments. After you let it sit for a few minutes retune it to standard tuning as the pitch will have changed slightly due to more or less relief and start again. Here is a link that explains how to check your relief and what you need to do to correct it.
http://www.fretnotguitarrepair.com/repair/acoustic-guitar/truss-rod.php
Remember that only after your neck relief is set properly should you adjust the action or string height using the saddle and nut height.
The other thing I do with guitars that have been cooped up in their cases for a long time, especially if they are still in NOS condition like yours and have not been properly "played in" yet, is to Let the guitar sit out on a stand when you are not playing it to let it breath a bit. I find this extremely helpful to allow the guitar to acclimate to its new environment. Your guitar is made out of wood which was once a living thing and it still changes its characteristics according to temperature, humidity, and other environmental factors. You will notice that with a few days of being on a stand in the house that it will loosen up a bit, at least in my experiences it does.
Best of luck with it and I am positive it is just a matter of making a few small adjustments to it to get it dialed in where you want it.
TX