Upvote:3
The overstay might or might not be a big deal in Thailand but I don't think the passport thing makes any difference. It could have been a problem when entering the country β if the validity was shorter than 6 months β and you obviously need a new one to leave the country and enter Malaysia but that's it. You might want to hold on to your old passport to be able to document your date of entry (stamp/visa-on-arrival).