3 cores mean nothing, minecraft can use 1, ( a fev plugins can use more ), so an old cpu wont do mutch
start disabling your plugins 1 by 1 and you will see whats lagging,
my tps falls usually caused by dynmap render booster, take the almost constant 20 to 3-4
so try dynmap pause all and wait a while
also consider deleting redundant plugin, essentials protect/lwc( wont do mutch since for example a block breaker can scoop your chest up even if its protected )
oh and the 2 h rollback, make a scheudle on your admin page, to /save-all in every 10-15 mins, so even if you crash you wont loose a sh**ad of work