Download and install Livesplit 1.6: http://livesplit.org/downloads/

Download this component: https://github.com/wooferzfg1/LiveSplit.TimerPause/releases/download/1.0/LiveSplit.TimerPause.dll

Put the file of the component in Downloads -> LiveSplit_1.6 (the non-compressed one) -> Components

Launch Livesplit with your splits

Go to Edit Layout, add "Timer Pause", and double-click on it

Set the time to 3 seconds.

During a run, press your pause hotkey whenever you see a save.