I might have found a fix/workaround for the nailgun and scenario images VMTR issue.
For the scenario images it's simple enough, just open up the 'decls\typeinfo\dlc_1_scenariolists.tdef' file in a text editor and move the "mapImage" property definitions so they come before the "loadoutList" definitions for each scenario. so they wind up looking like this:
scenarioDecl scenario/ghosthideout {edit = { displayName = "#str_mapname_ghost_hideout"; scenarioMap = "GAME/wasteland1/ghost_hideout"; spawnSpot = "player_start_from_wasteland"; unavailableText = "#str_achievement_25_desc"; descriptionText = "#str_jobname_wasteland1_hagar_quell_bandit_threat"; requiredAchymantId = 25; job = "jobs/wasteland1/hagar/quell_bandit_threat"; mapImage = "textures/guis/icons/scenarios/ghost_hideout.tga"; loadoutList = "scenarioloadoutlist/dlc_1_ghosthideout"; scenarioLayers = "lay/veh/wlsplines,lay/job/wl1/always,lay/job/wl1/barricade,lay/job/wl1/barricade_pre_dam,lay/job/hagar/xbow_pre,lay/job/hagar/l1,lay/job/rcbase/pre,lay/job/dc/pre,lay/job/dam/pre,lay/job/hagar/always,lay/job/quest_nav,lay/job/hagar/d_nothing,lay/job/wl1/north_block,lay/sew/1/first,lay/sew/2/first,lay/sew/3/first,lay/sew/4/first,lay/sew/5/first,lay/sew/6/first,lay/sew/7/first,lay/t/1,lay/t/6,lay/t/7,lay/t/3,lay/t/12,lay/t/13,lay/t/15,lay/t/21,lay/t/22,lay/job/wl1/always_cm,lay/job/hagar/dr_d_lock,lay/areas,lay/jumps,lay/job/wl2/always,lay/job/ghost/threat,lay/job/hagar/ghostcar";}
It looks like when it is building the VTMR it's retrieving the unique loadout images from the loadoutList first instead of the map image so they end up in the wrong order for the rage VMTR.
For the nailgun it's a little more complicated, open 'md6\weapons\nailgun\nailgun.md6mesh' in a text editor... **Updated with a proper fix for the Nailgun**OK so I had a closer look at what was happening with the nailgun, turns out you don't need to mess with it's meshes at all. There's an asset that jumps into the place for the nailgun_base in the vmtr (models/vehicles/class2/buggy01bodypanels4, if you're wondering), that's why the textures are all screwed up on it and why moving that top shader to the bottom made the other 4 look perfect for me while the nailgun_base texture was still messed up.
To fix the nail gun for your mods open up "decls\skins\vehicle_buggy.skin" and comment out all the declarations for the robocola skin, something like this:
//#ifdef DVD3// robocola// {// "models/vehicles/class2/buggy01bodypanels" "models/vehicles/class2/buggy01bodypanels4"// }//#endif
There should be ten of them. Then go to your "generated\skins\m2\" folder and delete the m2 file for the robocola skin.
After that the robocola skin won't try and load into the _vmtr_dlc.vmtr file during build so the nailgun will get slotted into its proper spot and will view correctly in your mod. And you don't have to worry that removing the robocola skin is breaking the game or anything because it's supposed to occupy the last two slots in the VMTR layer and the way Rage uses it's own _vmtr_dlc.vmtr file means it's just as if it was left in and the game can still use it.