If none of your text or explainations contain brackets you can skip all bracketed text.

use strict;
my $line = " Jack and jill went up the hill to fetch a pail of water. 
+Jack fell down and broke his crown and jill came tumbling after.";
my $newline = $line;                # MAKE A COPY OF THE LINE
my @wordlist = ('pail', 'water');   # THE LIST OF WORDS TO SEARCH FOR

my %hash;
$hash{water}{explanation} = 'A clear liquid.';
$hash{pail}{explanation} = 'A cylindrical vessel with a handle that ho
+lds water.';

## FOR EACH WORD IN THE WORDLIST -- FOOTNOTE THE WORD
for (my $i=0; $i < @wordlist; $i++)
{
    my $currword = $wordlist[$i];
    $newline =~ 
    s/((?:[^{}]*?|\{.*?\})*)(\b$currword(?:ed|ing|al)?\b)/$1$2 \\footn
+ote \{$2: $hash{lc($2)}{explanation}\}/xi;
}

print $newline;
__END__
Outputs:

 Jack and jill went up the hill to fetch a pail \footnote {pail: A cyl
+indrical vessel with a handle that holds water.} of water \footnote {
+water: A clear liquid.}. Jack fell down and broke his crown and jill 
+came tumbling after.
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