This will give you the correct line number count. counting the newlines in the matched set isn't what you want, unless I misunderstood your code. - slurped file into variable $f and changed reference of $slurpedfile to the original input file.

hth
John

#!/usr/bin/perl
$file="theinputfile";
undef $/; #In order to read the whole file at once
open(F,"$file");
$f = <F>;
my @matches =  $f =~
m{
     ( /\* .*? \*/) | ( \/\/[^\n]*)
     | " (?: [^"\\]* | \\. )* "
     | ' (?: [^'\\]* | \\. )* '
     | . [^/"']*
   }xgs;
@matches = grep {defined $_} @matches; #get rid of undefs
my $linenum = 1;

foreach my $match (@matches) {
#        $slurpedfile =~ /\Q$match/;
        $f =~ /\Q$match/;
        my $before = $`;
#        $slurpedfile = $';
        $f = $';
        my $matched = $&;
        $linenum += $before =~ tr/\n/\n/;
        print "Line $linenum\t$match\n";
        $linenum += $match =~ tr/\n/\n/;
}
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