If you had failed to check in 90 day at any point, and you left, when you reenter Thailand, guess what? .. you are all clear. Noted that when you reenter you should do the TM.30 report first, as your newest 90 check in will sometime requires the Tm.30 first

If you fail to check in 90day, the only problem is when you try to renew something they might spot it. Or if you are arrested, they would have a reason to fine you for late 90 check in

To change from 30 day visa to a non O visa in Bangkok, you must wire transfer bank to bank for 800,000 B from aboard. When you turn in all the required paperworks in Bangkok, one of the paper work is the Credit Advice aka reciept of internationally wired transfer. To get a non o, this fund doesn't need to be in Thailand for 2 months at all. Immediate transfer is accepted. But when you go for a 1 year retirement, yes that fund must be kept at least 2onths prior to application date.

If documents completed, make online booking time of your application in advance.