Seems like I remember Chris saying that losing the mod_perl dependence was something relatively high on his TODO list. While I haven't looked at the code lately, it might be something easy to do. I remember one application that "required" mod_perl because it used $r->print() and Apache::Request methods that have CGI counterparts. I think I spent 10 minutes changing it to run under CGI.
At a minimum you should probably look at the frameworks Perrin mentioned because they have a lot of very useful functionality you might be able to implement for your framework.