I am confused about the type of scale this is. It seems that the white fluff occurs in different spots than the brown shelly things. The images with the swab are - taking some of the cottony stuff off - then alcohol dipped - then smushed.
You may have mealybugs as well as armored scale.
https://www.gardeningknowhow.com/plant-problems/pests/insects/control-plant-scale.htm
https://www.gardeningknowhow.com/plant-problems/pests/insects/what-is-armored-scale.htm
https://www.gardeningknowhow.com/plant-problems/pests/insects/what-is-soft-scale.htm
I just purchased japanese yew seeds but I have a doubt whether the toxin in the seeds are removed or is it still poisonous
Yes. The fruit on the outside is not, but the seed itself is toxic.
https://www.gardeningknowhow.com/ornamental/shrubs/yew/japanese-yew-plants.htm
I would like to cut my yew tree down to perhaps 4 feet from its current height of about 10 feet. I would then trim it to maintain that height. Will this decimate the tree or will it continue to grow?
It's best to wait till it's dormant to prune it. Late winter would be a good time. Also, take a couple years to reduce the height. It will continue to grow, but the height shouldn't grow too quickly. Here is more:
https://www.gardeningknowhow.com/ornamental/shrubs/yew/pruning-yew-shrubs.htm
I have planted a row of yew to form a hedge. I read about clipping the new growth to stimulate more thickness/fullness, but how can I encourage more growth between each bush to form a more continuous wall of hedge?
You can clip all sides to make the shrub bushier. Wait till the height you want is achieved before clipping the top. Here is more:
https://www.gardeningknowhow.com/ornamental/shrubs/yew/pruning-yew-shrubs.htm
My tree man suggested cutting down and grinding out the stump rather than digging them out. Will this impact the new planting adversely?
Grinding a tree stump is a good way to keep the tree/shrub from returning. It shouldn't affect the new plants.
https://www.gardeningknowhow.com/ornamental/trees/tgen/kill-zombie-tree-stump.htm