I believe you are allowed to switch between input devices when ever you want( or maybe between loads or something) as long as you dont use both at the same time so what you are trying to do should be ok

I think that you are allowed to swap whenever, its just that you are not allowed to be using them at the same time

When we are doing a very long run, say bearger default preset, are we allowed to pause the timer and have some breaks in between the run as I think that when you play 10 hours straight you would want a rest in between. Also, can we kill (and post it on speedrun.com) more than one boss in one run?

I could too but I do not know how to access the files where you type in the seed so I will probably not be one. sorry

Do we have to kill a level 3 shadow piece in this category, kill 3 shadow pieces of any type or just kill a shadow piece?

Can we use the mod '[API] Gem Core' https://steamcommunity.com/sharedfiles/filedetails/?id=1378549454 for our runs?

Are we allowed to use wilderness mode or endless mode and have PvP on?