As you work inside Thailand you only have to show your tax and sso payments of the last 3 months from you and the Thai staff needed to get the work permit.
You can apply during every 90 day of stay you got on entry with this visa and do not have to wait until the visa itself expires
That is correct, BUT as soon as your wife applied for and been issued the 1 YEAR Extension of Stay based on being over 50 years of age, which means she has long stay in Thailand you are able to apply.
NOT as you asked during the 90 days visits with a Non Immigrant O visa.