tirsirrak: See this is my second play through first time i may of picked to not let jonny take over. However on this play through I started as corpo and did none of the main quests after heist till I had 'cleared the map' I am now starting the main quests, chipin in. Never fired.
oh well then no one else has this issue it must be something I am doing. Will look for it once more on my third play through.
Tapeworm is in 4 parts - dialogues that trigger after "Automatic Love", "Transmission", "Life During Wartime", "Search and Destroy". After that it will show up as a quest marker at the Afterlife.
I replayed the talk with Johnny in the hotel room where he gives you the dog tags and told him No Deal about letting him take over. The quest marker is still there, he just says take me to the Afterlife if you change your mind.
So you should be able to do it as long as you get the scene where you get the dog tags.