The shock product you used is calcium hypochlorite (cal-hypo) which adds calcium hardness (CH or TH) to your water. Vinyl pools don't really need that and, in fact, too high a level can be detrimental. Have you added any other products to the water? I'm curious as to how the CYA (stabilizer) produced a reading on the test strip.

Six hours on the pump and filter sounds reasonable. I run mine on a timer during the night when electricity is cheaper. Yes, you can run it with the cover on as long as the cover doesn't obstruct intake and return.

Get some regular 6% household bleach and add 1 qt each evening; this will add about 3 ppm chlorine to your water. We cannot stress the importance of a drop based FSD-DPD test kit strongly enough. It's the only way you can know with some certainty what your water chemistry is.

Happy swimming!