It has been nearly a month, and I'm still struggling with this. I have not been able to figure out how to write a filter that will recognize the Cisco text and prevent it from being filtered. I would appreciate any further insight that anyone might be able to lend.
As a side note, I recently made a change that Joseph Rezeau made in the following post: http://moodle.org/mod/forum/discuss.php?d=153907
After changing FORMAT_MOODLE to FORMAT_HTML, on line 540 in mod > lesson > view.php (1.9.9) the Lesson Branch Table no longer gets cleaned! Wonderful! I can now use my Cisco text! It is great that it now works in Lessons, but I need it be able to work in Forum Posts, Labels, etc... I also need the "students" to be able to use the code wherever there is an html area. I assume that this means I'll need a filter, but I'm willing to try anything.