I'm sorry for not getting back to this sooner. I had the OWC with the Oracle programmer and we were told to continue modifying the custom project security package. The only difference going from 11i to R12 would be which package. 11i has a package named pa_security_extn.check_project_access and in R12 there are 2 packages named pa_security_extn.check_project_access and pa_security_extn.custom_project_access. We were told to continue modfiying the pa_security_extn.check_project_access to allow for our custom project access to continue working in both the java web pages and the GUI forms.
Hope that helps!