So, i have created my own copy of a nirnroot activator, and deleted most of the code, so the entire plant just deletes itself and you get my custom ingredient in your inventory, how could i go about making a quest progress once i pick up the plant?

Couple of ways:

1)

If PlayerRef.GetItemCount(YourItemID) >= 1 )   YourQuest.SetStage(10)EndIf;Attach this to your Quest Script

2)

Event OnActivate(ObjectReference akTarget)  If ( akTarget == PlayerRef )     yourQuest.SetStage(10)  EndIfEndEvent;Attach this to your activator/flora

3)

I believe there's a way to use an Inventory Filter to do this, too... But I have not tried anything with that, so do not know exactly how it works.

Depending how your Quest is scripted, it might be better to go with 2 overall; that way you're not polling the player continually, and it only advances specifically when you take the item; assuming 3 works the way I think it does, that would be the very-best, but I've no idea how to do that, or if I understand it correctly, so maybe someone else can add more details there