Without running your script and checking the total of the sequence myself one guess would be that it is not generating the sequence you think it should be? Try running it with a smaller subset of characters (like two or three) and see if generates the sequence you think it should. Also you should be able to get a match on a shorter target first before running on the full length target.

Have you manually checked that the checksums are correct? It seems like $sum = $sum+($index1 * $n * $i)*($index1 * $ +i * $i); would generate an unusually large number. Note that since perl uses doubles and a lot of old C code uses ints that are 16 bits if your checksum algorithm relies on a 16 bit wrap you are going to get garbage.