I thought I had this figured out.
I built a php.cgi, but rather than have a copy of php.cgi in the /cgi-bin/ dir for each domain I have. I create a sym link to a common directory so they could all use the same php.cgi ref. Only problem is they are now also using the same PHP.INI file =/ I don't know how to fix this problem.
When I ran phpinfo on each domain, it referred to the first domain's PHP.INI file