How do I “pick and choose” which items in the array I will sort, and make sure I leave the other items alone?

The trick here is to extract a list of the indices of the required subsets; sort those indices according to the appropriate criteria; and then build the sorted array by slicing the sorted array by the subset indices in their original order and the unsorted array by the subset indices in their sorted order.

To illustrate:

data:     iOrig     iSort
0: e20        0            4
1: b17
2: e04        2            2
3: r16
4: e01        4            0
5: b12
6: e99        6            6

@sorted[ @iOrig ] = @data[ @iSort ]
[download]

Thus, the subset from the original data is assigned in their sorted order to the sorted dataset overlaying their original positions; but reordered.

A simple example coded for clarity with lots of scope for optimisation:

#! perl -slw
use strict;

my @data = qw[
    alpha bravo charlie delta east echo exit foxtrot golf hotel india 
+juliet kilo lima mike
    november oscar papa quebec romeo sierra tango uniform victor whisk
+ey xray yankee zulu
];
my @sortedData;

my @rindex = grep{ $data[ $_ ] =~ m[r] } 0 .. $#data;
my @rsorted = sort{ $data[ $a ] cmp $data[ $b ] } @rindex;
@sortedData[ @rindex ] = @data[ @rsorted ];

my @eindex = grep{ $data[ $_ ] !~ m[r] && $data[ $_ ] =~ m[^e] } 0 .. 
+$#data;
my @esorted = sort{ substr( $data[ $a ], 2, 1 ) cmp substr( $data[ $b 
+], 2, 1 ) } @eindex;
@sortedData[ @eindex ] = @data[ @esorted ];

my @oindex = grep{ $data[ $_ ] !~ m[r] && $data[ $_ ] !~ m[^e] } 0 .. 
+$#data;
my @osorted = sort{ substr( $data[ $b ], -1 ) cmp substr( $data[ $a ],
+ -1 ) } @oindex;
@sortedData[ @oindex ] = @data[ @osorted ];

print for @sortedData;


__END__
C:\test>1111596.pl
whiskey
bravo
charlie
zulu
echo
exit
east
foxtrot
juliet
kilo
tango
hotel
golf
mike
yankee
november
oscar
quebec
alpha
romeo
sierra
delta
uniform
victor
india
xray
lima
papa
[download]

Notes:

• bravo and charlie haven't moved because they both contain 'r' and were in the required order to start with.
• east, echo & exit have remain in the same range of positions 4..6, but are reordered according to their 3rd characters 'h', 'i' & 's' respectively.
• whiskey is first because it: doesn't start with 'e', nor contain 'r', and ends in 'y'.
• papa is last because it: doesn't start with 'e', nor contain 'r', and ends in 'a'.