On point 2 no further action needed, being married to the mother at time of birth legitimised paternity. So your best bet is to apply for the 1 year extension based on Thai child as the 400k only has to be in your bank on the day that you apply

Thai driving licence is fine for domestic air travel

Extension of stay granted yearly

So if our visa is still valid we still need to do the 90 days report?

Do it online, use Google chrome

You are best off to sit tight in Patong and wait for news before the 30th which will come. There are many many people in the same boat. It's too hard to try and get anywhere in Phuket currently plus you have no need until 30th. You'd need a letter from the district office just to get out of Patong and you won't get one for this. They will just tell you to stay put

It doesn't sound correct that you paid for a reentry permit after you got back. This means that you didn't actually have a reentry permit when you left and this is why you were given only a 30 day stamp when you returned. If you did go to immigration after you got back and pay for a reentry permit you will probably find it unused stamped in your passport. Plus how did you do a check in in December and March if you had a 30 day stamp?

Additionally the ban on incoming passenger flights has just been extended to Saturday. So no one is coming in either foreigner or Thai