Anyone have experience with "tax reference number 9001"? I got that message called the number got a standard message and call ended. Due to shutdown maybe?

The IRS uses reference code 9001 to indicate a "Systemic error/issue". In other words, it's likely not a problem with your return. Take a deep breath, wait a day or two, then try again. The IRS won't start processing your return until at least January 28 anyway, even if they said it was accepted.