Reply To: B) The header has jumped from 60px to 165px deep.

Its actually the header widget area. When you add a logo, it activates this css code –

.header-image .site-header .widget-area {
	padding: 40px 0;
	padding: 2.5rem 0;
}

Notice – header-image .site-header .widget-area is the entire widget area all together. By default it adds 40px padding to the top and bottom. You can decrease this to a size that works for your site.