I tried to use the Holy Grail workflow by following the instructions in the tutorial. When I click on the Holy Grail wizard, I don't get the new yellow line that Gunther gets when he does it. Is that only available on the pro version, or am I doing something wrong?

No, it's available on all versions. You need a sequence that has been shot with the holy grail method, and you have to create the key frames first with the keyframes wizard (those orange triangles). Then try again.
If it still doesn't work, please send me the log file (info/log).

If I understand correctly, the Holy grail method is just increasing or decreasing the shutter time, and or ISO as the light levels change. Am I right?

Yes, exactly. Either manually, or with a special Ramping device like an Android Tablet with dslrdashboard or the ramper pro.
See: http://lrtimelapse.com/gear/#tabs-613-0-1

Here is the log file. Thanks for your help.
Please send the content of this log-file to support@lrtimelapse.com if you experience any problems.

[2014-05-19 11:01:05] DEBUG: Loading properties from C:\Users\Wrights\AppData\Roaming\LRTimelapse\user.props
[2014-05-19 11:01:05] INFO: LRTimelapse 3.3 (2014-03-25)
[2014-05-19 11:01:05] INFO: © 2014 Gunther Wegner
[2014-05-19 11:01:05] INFO: http://lrtimelapse.com
[2014-05-19 11:01:05] INFO: Java version: 1.7.0_51 (64bit) from Oracle Corporation
[2014-05-19 11:01:05] INFO: Running on: Windows Vista locale: en_US
[2014-05-19 11:01:05] INFO: 64 bit
[2014-05-19 11:01:05] INFO: ------------------------------------
[2014-05-19 11:01:07] INFO: Licensed to: Melani Wright, 84737 - Private License.
[2014-05-19 11:01:09] DEBUG: Initializing directory chooser.
[2014-05-19 11:01:10] INFO: Done (dirchooser)...
[2014-05-19 11:01:12] DEBUG: Launching ExifTool: C:\Program Files (x86)\LRTimelapse 3\exiftool.exe
[2014-05-19 11:01:14] INFO: ExifTool: 9.54
{ready}
[2014-05-19 11:01:14] DEBUG: Exif Tool available.
[2014-05-19 11:01:14] DEBUG: DNG Converter not found.
[2014-05-19 11:01:14] DEBUG: MPEG Encoder available.
[2014-05-19 11:01:14] INFO: Detected Screen size: 1280 x 1024
[2014-05-19 11:01:14] INFO: Newest version: 3.3 (2014-03-25), current Version: 3.3 (2014-03-25)
[2014-05-19 11:01:25] INFO: Loading directory: C:\Users\Wrights\Desktop\Melani's pictures\Timelapse\Pteradactyl tracks
[2014-05-19 11:01:34] INFO: Done loading directory.
[2014-05-19 11:01:34] DEBUG: Timestamp Data complete!
[2014-05-19 11:01:51] DEBUG: interrupting loadPreviews...
[2014-05-19 11:01:52] DEBUG: Launching ExifTool: C:\Program Files (x86)\LRTimelapse 3\exiftool.exe
[2014-05-19 11:01:52] INFO: Loading directory: C:\Users\Wrights\Desktop\Melani's pictures\Timelapse
[2014-05-19 11:01:52] INFO: Done loading directory.
[2014-05-19 11:01:52] DEBUG: Timestamp Data complete!
[2014-05-19 11:01:52] INFO: Done loading previews.
[2014-05-19 11:02:20] DEBUG: Launching ExifTool: C:\Program Files (x86)\LRTimelapse 3\exiftool.exe
[2014-05-19 11:02:21] INFO: Loading directory: C:\Users\Wrights\Desktop\Melani's pictures\Timelapse\Pteradactyl tracks
[2014-05-19 11:02:22] INFO: Done loading directory.
[2014-05-19 11:02:22] DEBUG: Timestamp Data complete!
[2014-05-19 11:02:58] INFO: Done loading previews.
[2014-05-19 11:03:07] INFO: Holy Grail sequence.

If you are in "Lightroom 3 Mode" (see settings) you might have run into a problem that I've just fixed in LRTimelapse 3.3.1. Please install that latest version and try again. Let me know!

It worked. Thank you. Now I have another question. When I process the video and play it back there are two spots where the overall brightness changes. How do I pinpoint the frames that need adjustment? Can I run it through LRTimelapse again?

You can do a two-step deflickering, I explained that in the ebook. Basically you load the "LRT_" sequence that you exported through LRTimelapse again and use deflickering.