Received my new LE6940 a couple of weeks ago, and while I was able to shoot a very tight group, it was quite a bit off to the bottom right.  I have two questions regarding this I hope someone can answer for me:

1) I'm thinking the iron sights should have their "baseline" adjusted so that I don't have to remember X clicks left and Y clicks up to get to 0.  If that's correct, can someone point me at the procedure for a 6940?  I have a sightmark .223 laser cartridge to make it a little easier.

2) Why wouldn't it be correct out of the box?  If car makers can machine a main bearing to 0.0005 tolerance on a production line, shouldn't a $1600 gun shoot straight?  

Thanks,
Dave

You use the front sight to adjust elevation and the rear for your windage.

Vision is specific to an individual.  A rifle that is zeroed for me may not necessarily be zeroed for you.
A sight that is mechanically zeroed (i.e. centered vertically and horizontally) may not be zeroed for you because of your individual sight characteristics.
I always have to adjust the sights a bit whenever I'm handed a strange rifle.

So...

1.)  The "baseline" is wherever the sights are after the front sight post (elevation) is adjusted and the rear sight (windage) is adjusted so that you're hitting where you want to at a specific range with a specific load.  Set it and forget it.  You should not be messing around with windage or elevation unless you want to re-zero with a different load (or you're making adjustments to compensate for a drastic change in range or crosswind).

2.) The rifle's shooting fine.  You just need to adjust the sights for you.  Or, to put it a different way, the human is the defective part.