How do I apply for a 60-day visa extension based on marriage to a Thai national while holding a Non-O visa?

For the 60 day extension, I believe you can get it any time. I suggest going to immigration and get the extension.

Okay.

There are two different things at work here and you're confusing them

A VISA is something that lets you apply to get IN to the country. It is valid for a certain number of days; like your 90 day single entry Non-O which was valid for 90 days from the date it was issued. <- That means you had 90 days to ENTER thailand on that visa when you would be stamped in for the number of days allowed by the visa (which in your case is also 90 days).

The ENTRY STAMP you got when you stamped into the counry is what lets you STAY in thailand. So you're good to stay until the 5th of Nov.

The stamp - IF it's a 90 day stamp. Count the days on the entry and exit by stamp. If it's 90 days, you're good. If it's not 90 days, go to immigration and get it fixed ASAP.