I feel your pain.
I ordered this bass back in late December
http://www.rocketmusic.net/cgi-bin/commerce.cgi?preadd=action&key=5824
received it around the end of February. tried doing an initial setup and the saddles bottomed out before I could get the action low enough for my preference. not a huge deal for me as I've shimmed numerous basses due to my liking of really low action. the bass was playing pretty smooth but I noticed that the G-string wanted to slide off the edge of the fretboard. held it upright and noticed 2 issues, the nut slot for the G-string was cut a little too close to the edge of the fretboard and the whole neck was mis-aligned. in the pics it doesn't look so bad but is much more noticeable in person. I thought the fender approach of loosening/aligning/re-tightening the neck screws trick might work. wrong. G&L has very tight tolerances for their neck to body fit. no wiggle room at all. people complain about loose neck pockets from fender, and in some cases is pretty bad, but a little wiggle room can be a good thing IMO. luckily Greg has been extremely helpful with this ordeal and he forwarded my concerns to G&L and got me a return label as well. I shipped it off the beginning of this month and hope it doesn't take as long as it has for you and others, but I'm pretty much in the same boat as you. they've got once chance to make it perfect, and if they don't, I'm asking for a refund and spending my money elsewhere. sorry for the long post, not trying to derail in anyway.