Using the timer is just a matter of using the <EQ+ command (I believe it <EQ+0128 but it might be 0256 I don't remember) and then using <STP at the end to save the time.
There's no spot in the profile for the timer though, and it doesn't reset upon dying and reloading a save, which causes two conflicting behaviors: When reloading a save after death the timer will keep going as if uninterupted by your death instead of jumping back to the position it was in when you saved.
The bigger problem though is when closing the game before reloading a save, as it will instead set the timer back to zero.
Without modifying game code (or doing a super gimmicky TSC system that disables loading profiles from the menu, only allowing reloads from death, like in my mod Genuine Plight) you're limited to timer challenges that don't involve any saving and loading.