Well, I'm going to answer this myself 
I removed /usr/local/apache/libexec/libphp4.so, since it is not needed anymore after upgrading to PHP 5. This took care of the libmysqlclient14 error:
MySQL Setup Script Version 7.0
Loaded cPPkgs::MySQL ok!
This is the cPPkgs::MySQL 5.0.24 installer for Linux.
MySQL 5.0.24 is up to date
I guess this function in /scripts/mysqlup is causing the problem:
Code:
sub checkphplinkage {
my ( @LIBS, @LIBS4, @LIBS5, %REQS );
if ( -e '/usr/local/apache/libexec/libphp4.so' ) {
@LIBS4 = split( /\n/, `ldd /usr/local/apache/libexec/libphp4.so` );
}
if ( -e '/usr/local/apache/libexec/libphp5.so' ) {
@LIBS5 = split( /\n/, `ldd /usr/local/apache/libexec/libphp5.so` );
}
@LIBS = grep( /libmysqlclient/, @LIBS4, @LIBS5 );
@LIBS = grep( /not\s+found/, @LIBS4, @LIBS5 );
foreach my $lib (@LIBS) {
chomp $lib;
if ( $lib =~ /(libmysqlclient.so.\S+)/ ) {
$REQS{ $1 } = 1;
}
}