Hi Dale j. I'm a bit surprised that more forum members have not replied to this.
If it was me - I would use a block to sand the base of the neck heel a touch, to get it sitting flat in the neck pocket, and see if that makes a difference. Maybe the neck should also be clamped to really test a good fit. I'm just not sure if this will fix the problem of the high e side though!
With the pickguard in place (if you use it), you may find the neck height is not much of an issue!
However, if you are worried about doing this, then contact Pitbull to see what can be done for you.
Also - if you look down the length of the fretboard does it seem nice and straight? The second picture on past 3 makes it look nice and straight - but it is hard to tell.