I left Myanmar via the Myawaddy - Mae Sot Border crossing. Straightforward, no hassles. Newly built smooth road. There is a 2nd land border crossing into Thailand east of Dawei. However, I did not overstay - sorry, can't help with that.
India-Myanmar border crossing at Moreh/Tamu:
Permits (in addition to the visa) need to be applied for a couple of weeks in advance. I got mine arranged by Seven Diamond Travel, Yangon, Mrs Mar Swe. MTT will very likely arrange for it too.
Application could be done by e-mail. Requirements: passport copy of the main page and the indian and Myanmar visa pages, a tour itinerary with the exact date of the intended border crossing at Tamu, 100 USD fees payable by Visa Card.
Guesthouses are available at Tamu and Moreh and again at Kalewa. None on the 150km stretch in between. The Kalewa - Monywa road was in very bad condition last year, 3 days, no known guesthouses. Alternatively there are inexpensive boats down the Chindwin River,leaving Kalewa around 3 p.m., arriving Monywa around noon the following day.