After making the world as small as possible (there wasn't any redstone or mob farms anyway), the world is around 300x300 blocks that we build on and mostly use as there is 5 of us that use the server. Also I have removed most of the plugins too. I tested it again today and after two minutes the server instantly stopped with no reasoning. Although I did notice that on the console the time is 32 minutes in front of my time (GMT) if that has anything to do with the issue I am unsure.
I don't know what else I can do on my side to fix the problem.
*Edit*
I just waited 20min to then be kicked off again in 2 minutes. This time the time was 63 minutes ahead and it did come up with "Can't keep up! Did the system time change, or is the server overloaded?" yet I've done everything I can do stop the server being overloaded? Is it the system time as it's so far ahead?