open HANDLE, $file
    or die "Couldn't open $file: $!\n";
print "Please Enter a word from $file: ";
chomp($word_1 = <STDIN>);
print "Please Enter a Word to Replace, $word_1, with: ";
chomp($word_2 = <STDIN>);

# Read the whole thing in.
undef $/;
$x = <HANDLE>;
close HANDLE;

# Re-open for writing, clobbering the file.
open HANDLE, ">$file";
# Change every instance
$x =~ s/$word_1/$word_2/g;
# To prevent changing substrings, it would almost
# certainly be better to use:
#    $x =~ s/\b$word_1\b/$word_2/g;
# But it's your call....
print HANDLE $x;