hmmm… I think maybe you didn’t do much to look for documentation. Try going to the plugin homepage.
http://maisonbisson.com/blog/bsuite
beyond the installation it is REALLY simple. The website has everything you need to know.
So it took some trickery, but the problem was actually pretty simple to fix. Apparently, the quotes are all escaped so the simple search wouldn’t find them.
by change these two lines
$bad_code = array('<p align="left">','<p align="center">','<p align="right">');
$good_code = array('<p style="text-align:left">','<p style="text-align:center">','<p style="text-align:right">');
to this
$bad_code = array('<p align=\"left\">','<p align=\"center\">','<p align=\"right\">');
$good_code = array('<p style=\"text-align:left\">','<p style=\"text-align:center\">','<p style=\"text-align:right\">');
everything works fine, now I have proper xhtml that functions as it should.