Is it possible to account for the height difference by adjusting the bridge saddles so they slant with the direction of the fretboard. Looking at a couple of forums it seems like this is a very common occurrence even with store bought guitars (if I understand your problem correctly).
http://www.tdpri.com/forum/bad-dog-c...han-other.html
Both my PBG strat and tele necks have different fretboard heights on each side, they both taper down 1mm or so on the treble side. Have you compared this neck to your other builds or other guitars? Also my LTD les paul copy has this same height difference. It's not a particularly high end guitar but you would think that for close to a grand this sort of obvious difference would be picked up if it were a major issue.