It appears that the site is now working? Here is the series of steps that I went back and did that finally ended with the home page working:
1. I prayed (not a joke)
2. I stopped the web site on IIS.
3. I recopied the WordPress 3.5 files OVER the existing files.
4. I started the web site back up.
5. I logged in as administrator (/wp-admin)
6. I updated all the plugins that said they needed updating.
7. I updated the Twenty-One Theme, even though I am not using it.
8. I went to the "home" administrator page. The page where it says "Welcome to WordPress."
9. I pressed the "Customize Your Site" button to see what came up.
10. Ta-Dah! My home page (front page) came up.
11. After that I cleared the cache in IE9 and Firefox and tried again. The home page came up at http://www.goodnewsjail.org.
I did a lot of fanagling around for hours before saying, "Okay I will start from scratch." Thus I went back and did the above 11 steps, ending in a working site (I hope).
I HATE upgrading, as it usually results in this high-anxiety, high-blood pressure night of doom. However, let me give credit where it is due. I am a Christian and took time out to pray and ask the Lord to lead me to a solution. Others prayed as well. On the heels of those prayers, things began to come together.
I worked 17 years as an aerospace engineer at Cape Canaveral and oversaw launch-critical systems that had to work during the count, else the mission was held. I had many times where perplexing problems came up, I was at a loss for answers (at my wit's end), and I prayed for guidance. We never had to hold a launch for any of the issues that I prayed about. Thanks for letting me share. God bless.