Heads up, I've released an update to my protocol handler sample on CodePlex: http://www.codeplex.com/MOSSPH/Release/ProjectReleases.aspx?ReleaseId=23453
This release includes several fixes and enhancements that makes building a Protocol Handler even easier than before. If you've tried to use the sample and gave up, take a look at the new sample as the new improvements may get you past some of the difficulties you encountered:
At this point I think it's pretty solid in terms of functionality and layout, let me know if you have any further suggestions.
Please access the new source using the "Source" tab. I haven't modified any of the documentation, so if you still need that please refer to release 2007.2
Let me know how it goes. Good luck and happy crawling!
-John