The IRC used to specifically say that second-hand materials were not allowed to be used. In one of the more recent renditions, that was removed and they now have an exception to use lumber without the grade marks -- in lieu of a grade mark, a certificate of inspection issued by a lumber grading or inspection agency will suffice. The National Institute of Standards and Technology website may help get you started.
Ultimately, the local building standards department will have to approve the material you are using. Many of the code officials are not familiar with the green movement, but they are beginning to understand and most are helpful once they understand where you are coming from. I would suggest meeting with the head code official and presenting your case. Often the local USGBC and the local NAHB chapter have good relationships with the code officials and can help with the process.