How do I handle visa and entry stamp issues for my time in Thailand with a tourist visa?

Yes, you just count 60 days from your last entry date stamp. That’s what visa exemption really is; -not a visa just a free stamp.

Everyone gets stamped in, but you might leave electronically without any physical stamp.

I am somewhat doubtful you actually went on a real "tourist visa" (that you got online from a thai consulate while you were in Malaysia before you came back)

and

it's far more likely you just entered the country on the 60 day free stamp (visa exempt) entry

I am also doubtful that you didn't get stamped in 😮. 99.99% of the time when people say this they just didn't look carefully at their passport 😕

Look again, page by page, it would just be a small red entry stamp that (if you came in free stamp entry) would say ผ.60-ม.17

Just so you understand, the "online eExtension" process works like this, you apply online, you upload all your documents online, you pay the 500 baht processing fee and the 1900baht extension fee then you GO to the immigration office to get the extension sticker stuck in <- so you still have to go to the immigration office.

What I mean is you might as well just go to the immigration office in your area and get the 30 day extension on your own for 1900baht.

At most offices you can apply for an extension when you have 30 days or less left on your current stamp (Jomtien and Samui only let you get it if you have a week or less left on your current stamp).

You don't lose any days applying early as the 30 day extension is added to your current stamps expiration date.