@RoyBatty I need FormID of references REFR of trees, not tree objects. Are there a lot of trees out there that don't switch properly? I guess they mostly work fine except for a few trees, so I need to check that particular references.
Checked monorail lods, looks like they share lod textures with New Vegas, but the textures are different! This messes UVs completely on FO3 monorail models
http://i.imgur.com/VF5UqIk.png
You need to unpack monorail lod models and their lod textures from FO3, rename textures to something different (or better copy to a different subfolder) and update textures in nifs. Press Ctrl+F3 in FO3Edit and enter Architecture\Urban\Monorail\
Fix all _lod.nif files from there. Thankfully meshes themselves do not conflict between FO3 and FNV.
@EssArrBee
Guideline on how billboards should be named, don't forget to set Has Tree LOD on records if absent. Actually lodgen scans all records that have that flag and checks for existing billboard files, that's why there are so much "missing" warnings when generating Trees LOD. I had to do that because the atlas is common for all worldspaces in fallouts unlike Skyrim, I must add all possible trees on atlas, not only used in particular worldspace.
http://afkmods.iguanadons.net/index.php?/topic/4051-wipz-tes5lodgen-for-trees-lod/
I use NifScope 2 alpha with shading (Alt+L) to grab billboard images using my own tool
http://www.nexusmods.com/skyrim/mods/60733