If your toons are A,B,C,D,E, you can run it 5 times like this: ABC, ABD, ABE, CDE, CDE. Then each toon would run exactly 3 times. If you want double that amount, run it 10 times, 15 times, etc, basically any multiples of 5.

For farming JP, I do think it's more efficient than LFD because:
1. You get 168x3 jp for 12 minutes of work and it gets pretty mindless after a while hopefully. Mindless = easy = can do it while watching TV
2. You're not inconveniencing anyone. I don't know, but I get nervous everytime I run LFD with other people not in the team, because while I'm sure I'm pulling my weight (dps or otherwise), other people may not be as open minded, and there's already a stigma against multi-boxers in general.