Ok, so I want to do a run, or maybe a few. My questions are as follows: Is it the mods that time it, or how do I set up the timer for the run. following that, are we allowed to have the max energy for the runs ... I'm assuming this second question is a yes, and should be put into game rules

Yes you can have max energy iirc As for timing it depends what you want to run, if you are planning to run individual levels then they go off of the in-game time displayed when the level is completed. If you are planning to do the area/full game runs, then the timing is simply when it says start on the first level to the end of the last level. It is recommended that you time it yourself, though mods will often retime runs when verifying.