If you apply for an OA Multiple entry visa, you can show AUD 54,545 in an Australian account (which is a lot more than 800K THB). For a NON O (retirement) visa obtained in Oz, you need to show AUD 2000. If you will obtain a Non O visa based on being over 50, in Thailand and then a 1 year extension of stay, you will need to transfer 800k into a Thai bank account.
It also does seem to make a difference if there is time spent out of the country in between tourist visas or visa exemptions. Visa runs, as you mentioned, where you jump a border, get a visa, and come straight back, or a border run with an exemption, is a good way to attract the wrong kind of attention.
Why are you just thinking of this now? You can renew a passport well in advance if you plan it. I had the same issue with mine. Renewed it 9 months before expiry and got the extension stamp transferred.
You most certainly did overstay. You could try to pay the overstay at immigration, then if they let you, apply for a 30 day extension. Then also if they let you, apply for a 60 day COVID extension. Not sure how much of an issue the overstay will be for all of the above.
What is your NON O based on? Is it marriage or children? Go for the 60 day visiting family stamp. If other, then you would have to go for the year extension of stay, if you have the funds.
I wasn't aware of the masters degree part. Although that is not confirmed yet anyway, and I would doubt it will be a requirement for those just working online. I did read though, that the proposal for the cost of this visa is 10k Baht per year for a 5 year visa, and then a further 5 year extension. Not bad for those who can get it...!