Please note the prominent warning in the lighttpd configuration file:
###############################################################################
# FILE AUTOMATICALLY OVERWRITTEN BY PI-HOLE INSTALL/UPDATE PROCEDURE. #
# ANY CHANGES MADE TO THIS FILE AFTER INSTALL WILL BE LOST ON THE NEXT UPDATE #
# #
# CHANGES SHOULD BE MADE IN A SEPARATE CONFIG FILE: #
# /etc/lighttpd/external.conf #
###############################################################################
As another user pointed out, you can make a permanent and non-conflicting port change in file /etc/lighttpd/external.conf.
There is an existing feature request for our installer to be aware of existing lighttpd installs.