Hi guys

I've repainted my 84 and am in the process of putting all the pieces together. I have a few questions about covering the holes in my passenger side door. ( BTW: the door is from a 964 or other later replacement as it has oval window frame cover plugs rather than the two round ones)
One: I found this rubber plug fallen inside the door but have no idea where it came from. Anyone know where it's from, and why it's so large compared to it's retention barb? Is it a bumper for the window mechanism or something?
Two: I have this huge hole in the front edge of the door (same diameter as the rubber plug above, incidentally). Can anybody tell me what this is plugged with? I can't imagine it was supposed to be open like this... it would let all sorts of weather/crap into the door.
Three: These holes have always been open. I could plug them with 3mm trim plugs, but are they there for a reason? Look like screw holes to me. Anybody have theirs covered?
As always, thanks for all your help over the years here!