Do the "failure-to-file penalty" and "failure-to-pay penalty" apply when amending a timely-filed return after the deadline?

Yes, failure-to-file doesn't apply because you did file -- even though you made some mistakes; that penalty is for not filing at all i.e. ignoring or defying the law. (There are some cases where they can treat a facially unresponsive return as not filed at all, but they only do this for the nutcases who file things like "I don't have to pay US taxes because I am a citizen of Jupiter and the US doesn't control Jupiter". Given you know they processed your return, it was not rejected.)

Notice 746 references IRC 6651 which you can see applies the failure-to-pay penalty in two cases:

(a)(2) if you 'show[] tax' on a required return (which is necessarily an original return, because those are the only required ones) and don't pay

(a)(3) if tax was 'required to be shown' (on your original return) but 'is not so shown' -- which is your case because of your mistake -- then the penalty starts only 21 days after they demand payment from you, which will or would occur only after they process and post your amended return (which for paper during filing season will probably be 3-6 weeks).

Moreover even if FTP did apply you would almost certainly qualify for reasonable cause abatement as provided by the law -- from your description it's clear you tried in good faith to determine the correct tax, and paid the amount so determined; I believe that's reasonable cause right there -- and in the unlikely case that failed, assuming you haven't had other recent problems you didn't mention, you absolutely qualify for first-time abatement provided by policy (even though it's on the website under 'small business and self-employed' it applies to all income-tax payers, except I'm not sure for corporations).

Yes you will have to pay interest; that's required by law with only very limited exceptions like military in combat zone. OTOH Treasury market rates have been clamped near zero since 2008 by the Fed's 'quantitative easing', so the IRS interest rate is and has been only slightly over 3%, and 3 years interest will be about 10% of the late-paid tax.