If your nut is aligned, it may be your neck is not on straight. Being that is NOT a Warmoth body there is a decent probability that the holes are not perfect and the use of the warmoth neck is making it go out of alignment.
Looking at it your heel, the bottom needs to move over to the left. Since that part of the photo is cut off, I am not sure how much room you have. It does not take much.
You can loosen you neck bolts, just back them out a bit. With the guitar laying on its back, slightly push the neck from the low E side towards the high E side. This may straighten things out. You can then use a business car or suck to fill the small gap you may have created on the high E side. The tighten the screws and cut out the showing card.
If it is WAY off still, you can take the neck off and take off some material on the low E side. This however may cause a need to re-drill some holes. Lets hope it not that bad.
Remember...this is all IF YOUR NUT is aligned like Cagey said.
I have several "Factory" guitars I have had to do this with when setting them up for a customer. Lots of the Mexican EVH guitars have this issue...not sure how they do not fix it.