So, as you suspected, you're probably going to have to adjust something a bit to make that neck fit and intonate.
This is actually not a Warmoth, well, not made by them anyway. It could be an exact copy, really not sure about that. I bought it from a guy who had it made for him, he just decided he didn't want it any longer.
So, the guy i bought this from, I was chatting with him this morning, he told me that not all necks are the same, as depicted in this photo
http://s37.photobucket.com/albums/e64/heem...nt=IMG_0888.jpg
Got me thinking, rather than modify the body, I can simply cut into the maple neck (leaving the fretboard in tact). I squared up the neck cavity, it reduced the length from nut to bridge post by 1/4". However, it's still 5/16" too long. So, I was thinking about cutting 5/16" off the maple (again, leaving the fretboard in place).