I'm not sure about user deletion logging, but if you uncheck the "really delete users" flag in Administration, Site Settings, then you won't accidentally lose users if you're concerned of that.
Some features in the system capture last updated datetime/last updated by information in the database, since mojoPortal 126.96.36.199. This was introduced along with the Recent Updates RSS feature. The HTML feature tracks that for sure.
The best thing to do is look at the mp_ tables in the database, if you have that capability, to see if the features you want to audit have those fields in place.