I was on education visa for 2 years. I applied for DTV in Feb at Hanoi which took 5 working days excluding the day of submission and got approval. You should tried that.
Me and my wife usually do the 90 report for ourselves and the kids. We just brought their passports with us without needing to bring them. Hope it is helpful.
Will be best to call the immigration directly if you are in the country or have a Thai friend call for you. From what I understand is that, when you have new passport - you have to go to immigration and request transfer of visa from old passport to new passport (just need to fill in the form with old and new passport). I heard that a year back someone apply for visa and got rejected because he still has his education visa although it is already expire. And he need to cancel that (expired visa) before applying for a new one. Yes, rules are changing all the time and better check with immigration. They are now pretty much responsive and speak good English as well.