Compared with file I/O manipulating hashes is cheap. Something like this perhaps:

use warnings;
use strict;

open inFile, '<', "accts_to_exclude.txt" || die "Cannot open accts_to_
+exclude.txt";
my %excludeList = map {chomp; $_ => undef} <inFile>;
close inFile;

open inFile, '<', "list1.txt" || die "Cannot open list1.txt";
my %acctList = map {chomp; $_ => undef} <inFile>;
close inFile;

open inFile, '<', "list2.txt" || die "Cannot open list2.txt";
my %diffList = map {chomp; $_ => undef} <inFile>;
close inFile;

open inFile, '<', "list3.txt" || die "Cannot open list3.txt";
my %nameList = map {chomp; $_ => undef} <inFile>;
close inFile;

open orgAcctList, '<', "orig_accts.txt" || die "Cannot open orig_accts
+.txt";
open outFile, '>', 'output.txt' || die "Cannot open output file output
+.txt";

while (my $line = <orgAcctList>){
    chomp $line;
    my ($filename, $state, $amt, $ttl, $account, $name, $invnum) = spl
+it /\t/, $line;
    next if exists $excludeList{$account};
    print outFile "$filename $state $amt $ttl $account $name $invnum\n
+";
    
    if (defined $acctList{$account}) {
        # do something (write this info to file1)
        next;
    }
    
    if (defined $diffList{$account}) {
        # do something (write this info to file2¡K)
        next;
    }
    
    if (defined $nameList{$name}) {
        # do something (write this info to file2)
        last;
    }
}
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