1) How do I change the background color - in the header, mid-section that goes behind the content area, and the bottom area that goes behind the footer area?
According to
Firebug:
The body background is {themedir}/images/s5_bg.jpg and is defined on line 6 of {themedir}/css/template.css
The header background is {themedir}/images/s5_bg_top.jpg and is defined on line 567 of {themedir}/css/template.css
The footer background is {themedir}/images/s5_bg_bottom.jpg and is defined on line 573 of {themedir}/css/template.css
2) There are extra white lines where I removed content from Top_row2_1 and other areas. How do I remove that white space. I check for background color in those spaces, but couldn't find an option to change it.
If you have updated Widget Context recently you probably have the (latest) version which has a bug that doesn't fully hide empty positions. The most recent club releases have a custom-modified version that fixes the bug, just grab the site-shaper for one of those and overwrite the widget-context plugin folder on your site with the one from the shaper.
3) I cannot figure out where the "Shape 4 Life Journey Church Design" post is located and how I modify it. Can you tell me which widget position that is in? Is the content in that widget tied to the "latest post"?
That is the content area; it's not a widget position at all, it's the area that displays the page content on pages, and the latest posts on a blog page. Just go to the "posts" area in the admin and make whatever edits you need.