Between salem and bangarapet,add tirupattur halt.Let it be a halt or passing through.Then map will get corrected.Then distance between SA and YPR will get increased to 250km -actual dist.It would force you to update TT acc.
.Also there is a method of adding slack time,i.e train goes very slow between the penultimate and last station.That is in your case,kalyan-dadar must take more than a hour.It is so that in due course of running,the train is surely going to be late and provision need to be given so that the train can reach destination on correct time.