Don't overwrite the Debian perl.

Every time I have had problems with updating a Debian box, it has been because the perl package got borked. Perl is deeply involved in holding apt together, and there is little nastier than trying to repair a half-done apt-get upgrade.

Once you go your own way (build an unpackaged perl), you should stay there. Use CPAN to add functionality to your own perl and apt-get for the Debian one.

Oh, and I don't recommend using update-alternatives for perl (pre-emptive advice). The alternatives system is also written in perl ... the circular dependencies can crush you.