What should I do if my extension request has been rejected and I only noticed after the deadline?

If your extension rejected, you should print and mail it. You have until April 20, 2019, to do so and it will still be considered filed by the deadline.  There is a five day grace period when your extension rejects.

Should I also send the payment or will it work via ACH I had requested?

Yes, you should also sent the payment.  If your extension was rejected, the payment information was not received by the IRS.