Hello Fred,
I've been doing the active exercises and following up with other lectures and phone sessions with Chunyi, and it seems to me that you are a bit tense during the exercises. That's why the pain - and not because of the exercises themselves.
My suggestion is that you do not try to be right. Do not think if "this is write or wrong" or "is my posture correct? am I straight enough?" or "oops, I moved and I shouldn't!" - all these thoughts can cause strain in our muscles when we are trying to do it right. So just do it. Even if the posture is not 100% yet, or if you need to move to relax the tension, do it! Eventually, with more practice, your body will automatically get the right position and will be comfortable when still - even without you realizing it.
The main point of SFQ is to bring us to relaxation and focus inside ourselves, a pure connection with the Universe. If one is tense or having charging thoughts, one must release those first. Only this way the body can truly relax and the energy can flow freely.
I personally don't believe that one we move a bit our body we interrupt the flow of energy. Energy is flowing anyway. And if we are already meditating, and in a better position than we usually are (like hunched over the computer, or driving, etc), we are already ahead!! The energy is already flowing more easily, right? And it will get better and better the more we relax and practice the movements.
You said "I try to focus on the torso, neck, and head being straight - and I also try to talk myself thru dropping that tension down into my knees, but still can't escape this." In my view, that's where the problem is.
Do not focus or try to focus on anything else besides your breathing. Breathing is the key here, for relaxation and being in the emptiness. Every time you try to talk yourself into doing this or that, like dropping the tension into your knees, you are demanding something from yourself. That of course creates tension!
Besides, you do not want to have the tension in your knees - NO!!!

Then you might develop a knee problem, just for excess of tension! Do not lock your knees, either.
So, to sum up: don't worry about your performance, just loosen up the muscles and joints, move if you need, because contracted muscles and joints get stiff and painful. Focus on your breathing, focus on peace, light, love. Stretch, shake, and relax your shoulders, neck, hands, face, before starting. And after, too!
And, put a smile on your face, as Chunyi always says!

Hope it helps.
Peace and love,
RCT