When ODFI originate files, where in the NACHA Operating Rules does it say that settlement has to be 2 days from origination?

See Appendix Two to the 2012 Operating Rules, Part 2.5 (Automatic Entry Detail Rejection Criteria). Return reason R18 (Improper Effective Entry Date)

The Effective Entry Date is provided by the ODFI (from the data supplied by the Originator), and becomes the Settlement Date for the transaction. For credit entries, it cannot be more than two Banking Days after the banking day of processing by the Originating ACH Operator. For debit entries, it can't be more than one day after the processing date.

U.S. Treasury entries are obvious exceptions.

Settle with whom??

Sorry, I don't normally touch this part of ACH, but I was asked by my bookkeeping department to see if I could help...

Our agreement with our ACH customer's says we need to receive their entries 2 business day prior to effective date. We are wanting to know if the 2 days is a requirement by NACHA or is that time limt set by the bank in their agreement.

For instance, ABC company normally wants their payroll paid out on Friday, so they send us the request on Wednesday. This week, for whatever reason, they sent it on Thursday, and still want payroll paid out on Friday. Are we in violation with NACHA if we still pay it out? Or are we just not doing what our agreement states?

You are fine. It can't be more than two days as quoted by John. Most banks do it two days in advance so they aren't scrabbling at the last minute.

Just to be safe, we specify two days in advance in our agreements with customers. But we often get files the day before their effective date and process them. NACHA says up to 2 days in advance on credit files and 1 day on debit files, so either way you're okay.
(We also get files sent to us a week in advance and the system warehouses them to process them in a timely manner to get to the RDFI on the eff. date.)