I'm guessing you're on the DTV which allows you 180 days stay each entry. 90 day reporting is required ANY time you are in Thailand for 90 consecutive days. So if you leave between day 91 and 180, the 90 days restarts on the day you return to Thailand. 90 day reporting is free and has nothing to do with your visa, so they will not check to see if you meet the conditions required to obtain your visa.
you do have to transfer the 800k to a Thai bank within the 90 days to get the 1 year extension (unless you use an agent) I'm not advising for or against agents, I'm just informing
If she hasn't booked anywhere yet I highly recommend Da Nang. 30 minutes away is Hoi An - a beautiful historic city and Da Nang has everything you need including a very modern international airport
We had no problem getting our 90 day non-o retirement visa in Vietnam. We used the Ho Chi Minh city embassy because we were in Da Nang. It took 5 business days. A little tip - keep your boarding pass from your flight to Vietnam - they asked for further proof of location and this is one of the things they asked for.
Here's my personal recommendation - come to Thailand on visa exempt and get 60 days, extend once for 30 more days (1900 baht at immigration). Then fly to Vietnam ($25 for a 90 day Evisa). Enjoy Vietnam and while you're there apply for the DTV. Problem solved.