We have a 3 day lag with our ACH as well. What we have done to our system is updated it to report the pending balance. This shows what we have debited without waiting for confirmation of it clearing. If the file has NSF'd or account frozen you will know before that 3 days anyways. This has help us to alleviate the calls and issues with merchants screaming about giving them there money back from pay offs, paid in fulls, and refinances.

Sean is correct in that the ACH system is on outdated system and so far the only solutions that have come up are companies like dwolla but are a hindrance in that the customer has to have an account on there end as well to bypass going through the reserve.