I would tend to agree with you on the bearing issue, some have had issue with the bearings, but not too many have had any issues with the motor and controller, other than not being able to interface it with Mach3
There are sources for upgraded spindle bearings here in the benchtop forum, I did this to mine as I am spinning it at 6000 rpm on a regular basis.
One more thing to check would be the pulley holder on top of the spindle, mine had the clunking noise, and still does to some extent, it was the interface between the splined part of the spindle and the pulley, I just loosely install the bolts holding the pulley so it can still wiggle a little bit and spin the spindle by hand while tightening the bolts, took about 75% of the noise away.
JTCUSTOMS


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. When I let it cool down, and did the same test in reverse, it was mildly warm, but not hot after a similar timeframe.