Problem: I can't change witdth of line after I have reduced the size of a combined object.
I should be able to select the whole thing and then set the width using the object button and fill and stroke selection then changing the stroke to a number I want.

Solution: I discover that the lines that were not changing did not have their stroke color set. I don't know how or why this setting would change since I am always using black, and it automatically chooses black, but after setting the stroke of the line to black, it scales again.

It is the way SVG behaves. You have all the children (objects in the group) defined as having no stroke color. Basically telling Inkscape and other SVG interpreters to display nothing. When you change the groups stroke color, it will change that only for objects that have a style property defined. Easiest way to solve your problem is to ungroup the object and then apply your stroke color.

Jelle