[Rendar]

Most, if not all of the lag and clipping came in Update 1.60 with the following change.

Adjusted - Before saving a house file, the game will, at the first save of the day, create a temporary backup file of that file. (This is mainly a temporary preventation measure to help deal with any houses that fail to save and load properly, while I investigate the cause.)

Try disabling this feature for an update, or even for just a little bit, and see how the server performs without it. Make a back up of the house saves prior to this to make it a fail safe. If the lag lightens up with this being disabled, we can safely assume it's this.