I guess the Immigration Officer told you that a 90 day report is not needed yet, but you will get a small document attached to your passport when you apply for the 1 year Extension of Stay.
IF the visa is still valid you can leave and re-enter the country to get a new 1 year of stay based on the visa but also depending on validation date of health insurance.
OR
you can apply for a 1 year Extension of Stay at local Immigration Office but than you need to meet requirements like funds in a Thai bank account and health insurance and copies of address registration and passports.
You have to look at a website of a Thai Embassy in a country where you like to go to apply for the Non Immigrant O visa based on being dependent on your wife with a long time stay inside Thailand.
What documents are needed are mentioned on that website, you have to do some research by yourself.
Correct, at the moment people do not get a TM6 Arrival/Departure card when entering by air. That also mean you do NOT have to fill in the number in other applications.
For the rule about being 90 days consecutive inside Thailand it is still the same, you have to be inside Thailand. When you are not inside Thailand it does not count, so on arrival you start again with day 1.