23hp mud buddy. Bearings on top and bottom say cool, but the muddle of the shaft get hot. Is there a bushing or a bearing in the middle? What would cause this?

Vibration could be an issue. How often do you regrease?

I just got the motor used, and greased it before I started it the first time. I didn't get any responses on this topic, so I just decided to go ahead and replace all the bearing and the U-Joint. We will see if that fixes it. Thanks.

If it was shaft whip you would know it, there could be a bushing in the middle that is not getting grease which would explain the excess heat, if you have not but in your new bearings and seals you could pull the shaft and see if it rolled true on a flat surface, you would also find out if there is an extra bushing in the housing that the previous owner could have stuck in there.