I am looking for instructions on how to setup a PEAR channel for our project so that we can deploy it with the pear installer. I have searched the web for a while and cannot fin
It looks like you are one of the few people who want to do this. That tutorial you linked to appears to be the latest (!) but the package is still somewhat in development. The documentation in that package is also non-existent. It looks like it's up to you to write the docs. Or maybe contact Greg Beaver; the author of the package and blog post you linked to. He also wrote a book about PEAR (albeit in 2006.) The amazon writeup mentions this:
Next, you will learn how to set up your own PEAR Channel for distributing PHP applications, both open-source and proprietary closed-source PHP applications that can be secured using technology already built into the PEAR Installer
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