I am testing installing modules we use in /usr/lib/perl5/site_perl/5.8.8 and leaving everything in /usr/lib/perl5/5.8.8 unchanged. This test looks good to me.

cpan> get  PHRED/Apache-DBI-1.10.tar.gz
[...]
cpan> make  PHRED/Apache-DBI-1.10.tar.gz
[...]
cpan> test  PHRED/Apache-DBI-1.10.tar.gz
[...]
cpan> install  PHRED/Apache-DBI-1.10.tar.gz
[...]
Installing /usr/lib/perl5/site_perl/5.8.8/Apache/AuthDBI.pm
Installing /usr/lib/perl5/site_perl/5.8.8/Apache/DBI.pm
Installing /usr/share/man/man3/Apache::DBI.3pm
Installing /usr/share/man/man3/Apache::AuthDBI.3pm
Appending installation info to /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/perllocal.pod
  PHRED/Apache-DBI-1.10.tar.gz
  /usr/bin/make install INSTALLDIRS=site -- OK

##</code><code>##

cpan> get  PHRED/Apache-DBI-1.10.tar.gz

##</code><code>##

o conf make_install_arg INSTALLDIRS=site
o conf mbuild_install_arg --installdirs=site
o conf commit

##</code><code>##

Perl patches do not break the perl modules we use.

##</code><code>##

The modules versions do not change while fixing the problem, e.g., installing them in site_perl.

##</code><code>##

We are running the same version of perl, 5.8.8, after the fix.

##</code><code>##

No perl applications need to be modified, i.e., everything can be found in the default paths.

##</code><code>##

No changes to the programming environment are required. 

##</code><code>##

Environment
RHEL 5.6-5.8.
Linux 2.6.18-308.el5 x86_64 x86_64 x86_64 GNU/Linux
perl, v5.8.8 built for x86_64-linux-thread-multi

##</code><code>##

root# yum list installed perl\*
Loaded plugins: downloadonly, rhnplugin, security, verify
Installed Packages
perl.x86_64                           4:5.8.8-32.el5_5.2     
perl-BSD-Resource.x86_64              1.28-1.fc6.1           
perl-Compress-Zlib.x86_64             1.42-1.fc6             
perl-Convert-ASN1.noarch              0.20-1.1               
perl-DBD-MySQL.x86_64                 3.0007-2.el5           
perl-DBI.x86_64                       1.52-2.el5             
perl-HTML-Parser.x86_64               3.55-1.fc6             
perl-HTML-Tagset.noarch               3.10-2.1.1             
perl-IO-Socket-SSL.noarch             1.01-1.fc6             
perl-LDAP.noarch                      1:0.33-3.fc6           
perl-Net-SSLeay.x86_64                1.30-4.fc6             
perl-SGMLSpm.noarch                   1.03ii-16.2.1          
perl-String-CRC32.x86_64              1.4-2.fc6              
perl-TermReadKey.x86_64               2.30-4.el5             
perl-URI.noarch                       1.35-3                 
perl-XML-NamespaceSupport.noarch      1.09-1.2.1             
perl-XML-Parser.x86_64                2.34-6.1.2.2.1         
perl-XML-SAX.noarch                   0.14-8                 
perl-libwww-perl.noarch               5.805-1.1.1            
perl-libxml-perl.noarch               0.08-1.2.1