As far as if Ink has turned or not, Skittles says that he's not a person anymore. This makes me wonder a couple of things.
1) Could there have been other things smuggled into the jail inside of those ball point pens? Kelly says that the authorities were investigating how the stuff was smuggled in. What stuff, ink pens? There seemed to be a lot of concern over ink pens. (The article says that the tattoos were inflicted, as if he was inked against his will. But, why would he pay someone to do it if he didn't want it done?) I think that maybe chemicals from his lab were in the ink pens.

2) If the pens contained performance enhancement drugs (perhaps to make himself a bad ass in jail or to increase his strength in order to jail break himself) then this would explain why there was police tape on his office door on Z-day. Remember, he committed the crimes in Santa Monica. Why would his office be a crime seen? Of course, they could have suspected that he may have left evidence there; murder weapon, bloody glove, photos of his wife and Jack Tripper. Also, the article says that it was to be determined if the tattooing would delay the hearing. I doubt that jail house tattoos are so uncommon that it would hold up a court appearance. But, the simplest explanation would be that the police tape was put there just prior to Z-day because they were investigating how chemicals were removed from there and smuggled into the jail.

3) Perhaps the drugs affected the way the Z-cooties work, limiting the effect on how, and/or how much he turns. He realized this and started to experiment with the chemicals and zombies. Maybe even ground zero.
Examples:
  • Some chemicals used on regular zombies increases their speed, others give them jumping abilities, others give the size and strength.
  • The chemicals are either used on those turned by biters and/or those turned at ground zero. Remember, Kalani said that CJ's convoy people said that the strange creatures came from there.
  • The super mod zombies, i.e. runners, jumpers behemoths... are still dumb zombies. So he decides to start fresh with unturned babies.
  • He experiments on infecting people and/or babies after giving them his Marion Jones Juice or Lance Armstrong Elixir. As opposed to drugging already infected people.
  • They turn, but retain some intelligence and their eye color. JUST LIKE HIM!