I have read the rules and it does say that you do not need to continue timing during loading screens, is it okay to do this and only upload time without loads or is it better to just keep the timer going the entire time and just submit with loads?

Also is it okay to have a few milliseconds where you load in and then start the timer? More rather as long as you don't move before starting the timer

Also, are autoclickers allowed when putting in items? I would assume no, but best to ask to be sure

I am going to answer the questions in the order they were asked

1. you could, and the mods would retime it for you (or at least they are supposed to)

2. Any movement like a mouse movement is counted as the time you first move. although you could do this, it isn't really going to help you that much. so to answer your question, yes

3. auto-clickers aren't allowed when putting in items especially in full game runs since your timer is going during the menus, therefore you would be cheating

Ahh, okay thanks