Having second thoughts on my HIM

Signed up for HIM in March of 2014. Had exactly 24 weeks to prepare so I bought Joe Friel's Training Peaks 12 week base followed by 11 week build. Having knee pain is not going away after about 30 minutes of running and its keeping me from completing many of my training goals. Short back story:

Started couch to sprint in July/August of this year and completed it at the end of September. Started to feel a lot of pain in my left knee about 20 minutes into my run (yeah, I was moving that slowly). Thankfully the pain switched over the right knee and I finished in pain. Severe pain the rest of the day into the night where I could hardly sleep. Continued but decreased in severity over a few days of ice and rest. Most likely culprit is IT band as the pain is on the outside lateral part of the knee and my IT bands are ridiculously tight. After a week I went for a short run and the pain started again so I cut my run short. This time it was gone within a day or so.

Fast forward to deciding to do the HIM. Swim was feeling strong, figured I could get my bike where it needed to be and I'd fix the IT band issue after a few weeks max. Well, it hasn't happened. I tried by starting my runs on an Alter G at only 75% BW and after 30 minutes my IT/knee started hurting. Continued anyway, figuring I'd "work though it". Was able to complete my short sprint workouts and ST but any and all runs over 30 minutes turn into knife stabbing pain. Figured the ST would help. I've also been seeing a therapist who does some specialized deep tissue work on my quads, calves, hips, IT, etc to try and loosen it up, in addition to foam rolling. I still can't do the longer runs and my training program is leaving me behind. Once the IT/knee has flared it affects my swim too.

The bottom line is that I'm starting to think that I didn't build enough base fitness before undertaking this training plan, having only been off the couch for a few months, and that I'm pushing my body into an injured state. Every day that I miss a run workout is a day I'm not following my plan, but I can't train in the level of pain that I'm in 30 minutes into a run. I don't know whether to try and train through it anyway, just do my bikes and swims until it gets better (assuming it will) and hope I have enough time to catch up once I'm healed... or to just stop everything and rest.. or pull out.

Race is now 18 weeks away.