The configuration dialogue I was referring to was the part when it asked

Please provide a full path to 'httpd' executable: [] /etc/init.d/apache2

Depending on your PATH environment variable, this might be the result of running which apache2. To check, examine the /etc/init.d/apache2 script and look for a line that points to the httpd binary; on my system, it looks like

# the path to your httpd binary, including options if necessary
HTTPD='/usr/local/httpd/bin/httpd'
#
[download]

which indicates the full path to the binary is /usr/local/httpd/bin/httpd. Similarly, the apxs script (which might be called apxs2) may be the result of running which apxs, or it might be under the same directory as httpd.

If you have multiple apache installations, you have to make sure that the httpd that you specify is the mod_perl-enabled one.