Hi Nicola,
That is great you are doing active exercises every day, and working with small universe meditation . The active exercises are very good for self healing. If you want to encourage the self healing process, either increase time spent in your qigong alignments, or add another session during the day. Active is very good, supplemented by small universe. That is a very complete program for self healing. Patience, consistancy, deeper immersion in the practice as is.
Another support can be learning level II. It is certainly okay to sword finger throat. That said, you aren't necessarily clearing the organ system relative to the sore throat. A complete level II clearing is better than itemizing a possible symptom of a deeper or more primary blockage. Everything is interconnected too, so you want to cover all the bases, always. Active exercises, small universe, does that. Level II has a complete clearing sequence too. "If" you were just clearing throat, also clear relative part of the spine first. I would either focus more on level I, or at some point, engage with level II more completely. Again, immersing more in existing practice is way to make exercises more effective. Good, better, best.
Before you meditate, do some active exercise, or more simply, just bounce for awhile. Wake up your physical body, get energy moving, "then" sit down and meditate.
Love,
Gallen