Here are some pics of my 2001 3.0i, built in June 2001. Generally dealer-serviced by the PO. No problems in this area before or after. These pics were taken after I had removed and cleaned the intake manifold as part of a head gasket repair.
The second pic below is probably the clearest of the area in question. Two holes are plugged, and one is not - at one point I knew what that thing did, but you can probably look it up better than I can remember.
I can see (and guess / remember) that both plugs I made were done with what I had. One is a rubber plug with some electrical tape to make sure it stays in place - I remember the original plug was there, but the rubber was cracking and disintegrating so this was a huge upgrade

. Similar on the other one. As said, no problems before or since.
Also, on removing things in the cowl area, I'll just say that all that plastic is extremely solid, easy to remove, and kind of amazing how much it opens things up when removed. So I would just start doing your work, but if you ever feel you'd get a better angle or access if something were moved, just take it out. Easy. I think the one extra helpful tool was a 19mm ratcheting wrench.