KT here. I'm a retired SEAL and worked as an instructor for a couple of tours. When I first started using the TRX I had all kinds of aches, mostly because I was trying to challenge myself too hard right from the get go. Which it sounds like you may have done starting at week 5. I know some of the exercises don't appear real challenging. For me it was my forearms that would get smoked doing the power pulls, but that didn't last long.
Right now your feet and shins are not used to holding up your bodyweight. Ease your self into these workouts. Those pains will go away and your core strength will increase over time. And your experience on the TRX will rock. Take your time and most importantly listen to your body.
As for the running program. Ease yourself into that also. It rocks, but it's challenging.