I’m not a android technical guy but it looks like a higher background process issue. Disabling unnecessary system apps is a good idea but disabling manufacturer system apps isn’t a good idea. I’ve doubts those appa you’ve disabled listed below. I should never disable these at all.
Google Play services, Google Play Store, Google Services Framework, Samsung Apps, Samsung Apps Widget, Samsung Link.
The system runs in full process when its looking for something and its not getting the right thing which it needs. Getting the phone hot is an indication for that, like its gets hot when playing large games. The cpu is running with full capacity. Also if the mobile data (3G/HSPDA) running constantly that is a plus point for making it hot and draining battery. Using WIFI most of the time consumes way to less battery.
Also check the RAM and CPU usage if possible, I doubt both will be high. And turn those apps on and keep all updated then do a factory reset, better by hard reset (not from setting menu). I hope this issue will be fixed.
Samsung Note 3: N9000 KitKat 4.4.2
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