Just to explain: TM30 stands for registration of a foreigner residing on an address in Thailand, so without having an address it is impossibile to report that you are more than 90 days inside Thailand and still living at the same address, this by using the TM47 form.
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.