missed file extension deadline 4/15, but made payment on 4/16/2026

"Or Just efile the return now and wait to IRS send notice of penalty?"

Yes.  Don't go out of your way to alert them that things were late.  Maybe the return will hit a computer that is really tired and not notice the issue.  Address the problem only if and when the IRS decides there is a problem.

I sent the Form 843 with the return when I missed an extension, but only because the return had to be filed on paper for other reasons - and it was a month late, not a day or two, and the penalty was going to be enormous. The 843 said it was my fault and if the IRS didn't waive the penalties, I was going to pay them personally, because those things were true. Historically, the IRS has waived penalties related to preparer error pretty freely, but they are so short-staffed now that it takes forever for anyone to read the letters.

For small-dollar stuff, I e-file without mentioning the penalty to the IRS and ask the client to send me notices if / when they get them.

Late filing and late payment are by-the-month penalties, IIRC, so a day is the same as a month. Interest should be minimal.