I think we wrote a message in the same time. I also think you're worrying about NI warnings a bit too much :P Really, none of these things are affecting the game and you will find LOTS of these things in the original BG(2), but sitting and fixing tons of things that do not affect the game feels a bit like an... unnecessary thing to do
Many of these things are really harmless, if you want to get rid of the "L#NIBRI" warning, change it to "Bridge" (I may also fix it at some point) in that script, but as I said, none of these 3 things is going to harm your game, and as you may see on the image I included, the wed fix is actually causing problems. The warning here is displayed because (IIRC) I removed the actual tiles/overlays and replaced them with burning fire animation, as the original area was using the old method for displaying such things (by using separate tiles rather than bams). The game is trying to display these tiles but they are not there so the game displays nothing in their place. For some reason the .wed files are quite moody and that works better than toying too much with those overlays (funny thing: neither NI or DLTCEP allows me to delete those, but their presence does not change anything so....)
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I spent 2 months importing IWDEE to BG2EE like this, only removing warnings. When I tested played, every thing was fine...