Here are my thoughts:
1. At this point if anyone alive and on "the list" turns out to be RJ, it will not be shocking at all. Partridge is conveniently dead, but they never showed the body or the autopsy or anything like that. Given RJ's reach and abilities, he should be able to pull this off to allay suspicions. I could see him seriously injure himself just to make a sale. Since RJ always uses pseudonyms, he can just change his name and start over.
2. He didn't kill Lisbon because he wanted her to pass on his "tyger tyger" message to Jane, and probably also because he likes her (although how much could a mass-murdering psychopath like someone??).
3. The tyger tyger conspiracy does not work for RJ. They are a separate entity, and are probably hunting RJ too. That's why RJ keeps tipping off Jane about them. They may not have been able to capture RJ, but they must make a formidable enemy to RJs own people planted throughout the government agencies. So for RJ, he and Jane have a common enemy in the conspiracy; and for the conspiracy, they and Jane have a common nemesis in RJ. If I were Bruno Heller (which I am certainly not, since I am sitting around speculating) this would be a nice way to create a new enemy for Jane to take down once RJ is dealt with, allowing for the series to continue post-RJ.
