After speaking to unnamed Academic Advisor at a Division One School who has handled waivers such as Jeremiah Masoli's in the past, the rules seem rather simple (at least when it comes to NCAA rules).
First off, Masoli would have to graduate with his bachelors from Oregon, which he is on pace to do. Secondly, a waiver would have to be sent to the NCAA where he requests the transfer for "academic reasons" - the key one being Louisiana Tech offers a master's program that Oregon does not. The "Taylor Bennett" rule (for Louisiana Tech fans) where it was automatically accepted is no longer on the books. The waiver must now be approved. Next, a graduate program would have to "accept" him at Louisiana Tech before the waiver can be filed. This is usually not an issue. But once again it must be a grad program that Oregon does not offer. Fortunately for Tech, the off the field issues are not taken into account by the NCAA academic review board in the waiver. It is not even mentioned. The review is strictly academic. Several players who have been kicked off a team and then graduate each year are given this wavier. A prime example is Kenneth Cooper from Louisiana Tech to UAB. Finally, since he has graduated he does not affect the APR of Louisiana Tech whatsoever.
Inside the numbers game with Masoli and the NCAA Masoli graduated high school in May 2006 where he finished as a late qualifier out of high school, so he sat out the 2006 season and eventually did make the grades for the clearing house. Since he did this, he was able to only play one year at City College of San Fransisco in 2007 and sign with Oregon in 2008. He played for Oregon in 2008 and 2009 while never using a redshirt year. As a result of not using a redshirt year, Masoli has has two years to play one. In other words, he can use his redshirt year and still play the following year.