I have loaded several mods but seem to be missing files, specifically those for opal, amythist, among others.

The specific files, in the data/meshes/n file are:

Ingred_Opal_SA.nif
Ingred_Goldnugget_SA.nif
Ingred_amythist_SA.nif

There are a few more, but I think you get the idea.

Anyone have a clue what mod failed to install correctly?

Morrowind.ini is:

GameFile0=Better Heads Bloodmoon addon.esm
GameFile1=Better Heads Tribunal addon.esm
GameFile2=Better Heads.esm
GameFile3=Bloodmoon.esm
GameFile4=Book Rotate.esm
GameFile5=GDR_MasterFile.esm
GameFile6=GIANTS.esm
GameFile7=MCA.esm
GameFile8=Morrowind Patch v1.6.3.esm
GameFile9=Morrowind.esm
GameFile10=TR_Data.esm
GameFile11=TR_Map1.esm
GameFile12=TR_Map2.esm
GameFile13=The Wilderness Mod 2.0 T & B.esm
GameFile14=Tribunal.esm
GameFile15=abotWaterLife.esm
GameFile16=A good place to stay, Ver 1,8.esp
GameFile17=Animal Behaviour.esp
GameFile18=AreaEffectArrows.esp
GameFile19=Better Bodies.esp
GameFile20=Book Rotate - Bloodmoon v5.3.esp
GameFile21=Book Rotate - Morrowind v1.1.esp
GameFile22=Book Rotate - Tribunal v5.3.esp
GameFile23=DM_DB Armor Replacer-Exp.esp
GameFile24=DN-GDRv1.esp
GameFile25=EcoAdj Ingredients.esp
GameFile26=EcoAdj(Sri+Ingredients).esp
GameFile27=EcoAdjCrime (Tresspass Edit).esp
GameFile28=EcoAdjDaedricDrops.esp
GameFile29=EcoAdjMerchantSkills (Disposition Edit).esp
GameFile30=EcoAdjMisc.esp
GameFile31=Fair Magicka Regen (one Percent).esp
GameFile32=GIANTS Ultimate Control file.esp
GameFile33=GIANTS_Ultimate_Official_Fixes.esp
GameFile34=LeveledMagicka.esp
GameFile35=MCA - Guards Patch.esp
GameFile36=Morrowind Crafting 2-1.esp
GameFile37=Morrowind Crafting Equipment.esp
GameFile38=Nature of Morrowind - rainforest of the bitter coast.esp
GameFile39=RealSignposts.esp
GameFile40=Statue Replacer - Marble.esp
GameFile41=abotWaterLifeTRaddon.esp
GameFile42=newarrows - crossbow realism.esp
GameFile43=newarrows.esp
GameFile44=vn_economy_GameStats.esp
GameFile45=vn_economy_ItemLists.esp

(Surely you mean "Ingred_Amethyst_SA.nif"?)

Anyway, the "SA" looks like it is from Sri's Alchemy. This mod (or its resources) is included in some other mods like Uvirith's Legacy, Silgrad Tower, Mori Mountain Estate, and perhaps others. Maybe you could search your plugins for references to those models, or if you have kept the original archives for your mods, list their files and search in there.