Well speaking from a purely mechanical point of view (land vehicles) it could be a number of things,,sounds like to create that kind of excessive heat the stuffing box is taking a strain it shouldn't,,or the prop shaft is oscillating maybe.
i'd say what you need is a heat sensor gun which can localy target an area,,use this to read the temp along the drive line,,bearings, seals
, etc,,,then get yourself a timing light and hook it up to the motor
and shine it along the shaft and see if you getting any variation in longitudinal and lateral travel. Best of luck,,