But looking at NI, is there a way to check what the AVATARS use when they equip it?? The icons and stuff show up well and good for the inventory, ground and descriptions ... just, the paperdolls and avatars have different icons
Paperdolls are usually .PLT files, though some (especially mod-added ones) are .BAM files. They're prefixed with a C, then characters indicating the race, gender and class of the character, then the armour level. So COMF1INV.PLT for example, is the unarmoured half-orc male fighter. Avatars use .BAM files with roughly the same prefixes, though not all paperdolls have unique avatars. So I think the half-orc uses the human avatar (chmf4a1.bam etc.) unless a mod specifically adds one (maybe 1pp does, not sure). Anyway, that is what you would change-log, though I doubt there are many other mods besides 1PP that change these. I'm not that familiar with it, so you're better off posting in its forum.
is this a case where overwriting was better than patching now??
No - why would it be? It was made patching for better compatibility with a mod that *does* overwrite - otherwise if they both overwrote, neither would be compatible with each other.
Regardless, Miloch, I found a "Pile of Bones" thing in the Nashkel Pass cave along with a medium shield ... AGBONE01??
I checked for any references to it in dlg's but found none ... Is it just flavor??
For now, yes. You can find some clue as to what (or who) it is (or was), but it has no "use" - it's a pile of bones after all. What did you expect?

It might figure in some future expansion, but that'll require the dialogue writers (Bookwyrme and K'aeloree) to show up again and do some writing.
EDIT: That same medium shield that I found above (Knight's Shield +1) shows up properly like the paperdoll icon on the avatar ... so this shows that only vanilla items are (un)affected 
You mean, they're the only ones affected by whatever mod weirdness you're talking about?

Got a CtD from an area added by Aurora ... reported to their forums
(turns out the exit referred to the TuTu areacode
)
Known issue already
reported and fixed.
Attached the result.txt generated by NI's "Find Illegal ResourceRefs..." function, there are a LOTTA files, I'll be reporting them to their own forums (when I get some time
) unless someone says otherwise
NI is not always the most accurate.
Stuff like this is bogus, because a lot of these sounds do in fact exist.
NI itself will tell you so if you expand the WAV folder:
File: AR3611.ARE Attribute: Sound 1=AMB_M34A.WAV
This stuff is bogus too. The VVC stuff is invalid because it should also look for BAMs of the same name (which do exist). The SPL protections do nothing if the spells don't exist (try running this on *non*-
BWP and you'll see a lot more so-called "misplaced references" for these items).
File: AGBOOT28.ITM Name: Gnomish Boots Attribute: Resource=SPENTACI.VVC
File: AGBOOT34.ITM Name: Stinking Gnomish Boots Attribute: Resource=ILY1.SPL
File: AGBOOT34.ITM Name: Stinking Gnomish Boots Attribute: Resource=SLOW.SPL
File: AGBOOT34.ITM Name: Stinking Gnomish Boots Attribute: Resource=SPENTACI.VVC
File: AGSTAF01.ITM Name: Staff of Swarming Insects +2 Attribute: Resource=SPIPLAAI.VVC
This might actually be legit - somehow the script may not have compiled for
BGT. Will check.
File: AGBARHOP.CRE Name: Boots of the Bar Attribute: Override script=AGBARHOP.BCS
Everything else in the AG* range (apart from AG4815 already noted) is not ours (unfortunately someone else was using this prefix, but it's too late for us to change and there don't appear to be any real conflicts).
So the other stuff you may want to double-check based on the above examples before reporting them as definite errors. DLG and BCS misreferences might be valid issues, but I'd be suspicious about other messages.