I have confirmed that the source of the errors in the newest program is definatly because there is a chance that a random combination of pulses could produce a valid output. So I think the only way to mitigate this is to also check the value and add that to the error.

Plus there are also times where the actual input data has some pulses missing off the end.  This is simply because I have not made the array big enough in the original creation.  A simple fix.