Re: Tags not separating
$tag = str_replace(',', '', $tag);
(That’s not the actual code you need, just an illustration.)
You could be doing this with a plugin, which is probably preferable as you don’t have to hack the core every time. The filter you want is probably
bb_tag_sanitize but I’m not sure. Check http://bbpulp.org/wiki/API/filters and http://bbpulp.org/wiki/API/actions.