Agreed, I think your use of polyquat was fine. I use it for the same reasons, to clear up a cloudy or dirty pool that my filter is inadequate to handle.
As to my previous post, I guess I should have said if your pool looks or behaves like it has a problem, it probably does. I have just learned that the CC reading is just one way to detect problems, but at least with my pool, it doesn't seem to always give an indication of CC when my pool is obviously getting green or cloudy.

The polyquat will be oxidized and decrease your FC content for a little while, not sure how long it will do that. Maybe someone else knows that can chime in.

It appears you are trying to maintain FC at shock levels, so keep it up and brush every day until you can maintain overnight. Don't get too frustrated, we've all been there!