to answer question 1, i'd just leave em alone because it only does anything if u have those modules. you coudl probably delete them but...if it aint broke dont fix it.
2. i have files for apache2 all over the place (Gentoo defaults)
i have a config file for /etc/init.d/apache2 in /etc/conf.d (filename is apache2)
and in it i had to add a line to get PHP4 support:
here is the entire file
# Copyright 1999-2003 Gentoo Technologies, Inc.
# Distributed under the terms of the GNU General Public License v2
# $Header: /home/cvsroot/gentoo-x86/net-www/apache/files/2.0.40/apache2.confd,v 1.5 2003/09/27 04:47:18 woodchip Exp $
# Config file for /etc/init.d/apache2
# An example from /etc/apache2/conf/modules.d/40_mod_ssl.conf:
# <IfDefine SSL>
# <IfModule !mod_ssl.c>
# LoadModule ssl_module extramodules/mod_ssl.so
# This means that the mod_ssl.so DSO module is only loaded
# into the server when you pass "-D SSL" at startup. To
# enable WebDAV, add "-D DAV -D DAV_FS". If you installed
# mod_php then add "-D PHP4". For more options, please
# read the files in the /etc/apache2/conf/modules.d directory.
APACHE2_OPTS="-D SSL -D PHP4"
i have stuff in /etc/apache2 for modules also. i normally dont touch modules accept to add the PHP4 support.