1) where exactly is the shard located
The Sormirbaeren Graveyard. It's exact location is randomized each playthrough. If you have enough Intelligence you can talk to Yngwar and the ferryman to find out where it is. While it is possible to obtain the shard by searching every part of every corpse, it is quite time consuming to do so.
2) if i return to the institute questline to gain access to the elevator can i just go to ocolus without compromising the original underrail storyline (which i have not finished and was saving for after i was done with expedition)
You don't have to do any of that, the entrance to Oculus is not in DC. You can access it from the caves near Rail Crossing, assuming you've completed the necessary quests.
3) i read about keeping the acorn and that only then i'll be able to get my hands on samurai armor and sword unique items. what are the consequences of this? do i have to fight my way out against AEGIS?
You will not need to fight Aegis, you can just tell them that you didn't find it. I don't know of any other consequences.
Personally I've chosen to keep it for myself, foolishly hoping that I'll be able to find some obscure way to open it.
Edit: I had to type this twice because the forum eats posts with special characters. Now that the word Sormirbaeren is going to be used here frequently it might be time to address that bug.