The broken muffler ended up being covered by Mahindra emissions warranty. When the dealer replaced the muffler, they also flashed the computer (took over an hour). Mahindra said my tractor was only the 2nd one made in that series (serial number 22GRH00002) so there were lots of updates for it. It does run smoother now and that should help with future problems. I was a little surprised it even used a computer for anything other than the instrument cluster.
Overall, I've been very happy with my tractor. At 56, it has saved my back many times.