i thought i may as well report this.
even though you stated not to clean your mod, especially with TESTool, i've noticed when your mod is active, there's a lot of anomalies with objects reverting back to vanilla state. now, i'm not sure whether is is intentional or not, but i thought i should share what i found.
i ran this plug-in through TESTool, and found out this mod has a lot of dirty object records. now, dirty object records are object records that are exactly the same as the master file entries, these tend to get saved in mods when a modder is placing and editing an object reference from that record, and hits the save button instead of exiting out of the object window. this is common mishap when a modder changes the scale of a reference, or assigns ownership, locks, etc...where they hit the save button when finished instead of simply exiting out of the object window. so they end up saving the object to the plug-in, creating the record of the exact same info as the master files. this can cause issues with mods loaded eariler in the loadlist where their changes will get overwritten.
here is the list of object records which TESTool reports as edited, and are exactly the same as the master files:
deleted STAT furn_anvil00 deleted STAT furn_web00 deleted STAT furn_web10 deleted STAT in_cavern_roots00 deleted STAT in_cavern_roots10 deleted STAT in_moldcave2_s_05 deleted STAT in_mudtrans_00 deleted STAT in_mudcave_08 deleted STAT in_mudcave_10 deleted STAT in_mudcave_28_1 deleted STAT in_mudcave2_00 deleted STAT in_mudcave2_01 deleted STAT in_mudcave2_06 deleted STAT in_mudcave2_s_01 deleted STAT in_pycave2_02 deleted STAT in_mudboulder00 deleted STAT in_mudboulder01 deleted STAT in_mudboulder02 deleted STAT in_mudboulder03 deleted STAT in_mudboulder04 deleted STAT in_mudboulder05 deleted STAT in_pyboulder05 deleted STAT flora_root_wg_01 deleted STAT ex_dwrv_alcove00 deleted STAT ex_dwrv_block10 deleted STAT ex_dwrv_block20 deleted STAT ex_dwrv_block30 deleted STAT ex_dwrv_ruin00 deleted ARMO dwemer_shield deleted STAT flora_root_wg_04 deleted STAT flora_root_wg_05 deleted STAT ex_dwrv_ruin50 deleted STAT ex_dwrv_pipe10 deleted CLOT common_robe_05_c deleted STAT in_dwrv_corr1_00 deleted STAT in_dwrv_corr2_00 deleted STAT in_dwrv_corr2_02 deleted STAT in_dwrv_corr2_03 deleted STAT in_dwrv_corr3_00 deleted STAT in_dwrv_corr3_02 deleted STAT in_dwrv_corr4_00 deleted STAT in_dwrv_corr4_01 deleted STAT in_dwrv_corr4_04 deleted STAT in_dwrv_wall00 deleted STAT in_dwrv_wall10 deleted LIGH orange_256_01_d deleted STAT in_dwrv_corr2_04 deleted ACTI furn_dwrv_tranny00 deleted STAT in_mudcave2_end deleted STAT in_mudcave2_s_end deleted ACTI furn_dwrv_beltdrive deleted ACTI furn_dwrv_dynamo deleted STAT furn_dwrv_fitting00 deleted STAT furn_dwrv_fitting20 deleted STAT furn_dwrv_fitting30 deleted STAT furn_dwrv_fitting50 deleted ACTI furn_dwrv_fitting40 deleted STAT in_dwrv_doorjam00 deleted STAT furn_dwrv_well00 deleted STAT in_dwrv_corr4_05 deleted STAT in_dwrv_shaft10 deleted STAT in_dwrv_corr4_03 deleted MISC misc_dwrv_gear00 deleted LIGH light_6th_brazier deleted ACTI active_de_bedroll deleted STAT furn_6th_ashaltar deleted STAT furn_6th_ashpillar deleted STAT furn_6th_ashstatue deleted STAT furn_6th_banner deleted STAT furn_6th_dagothsymbol deleted STAT furn_6th_troth_01 deleted STAT furn_6th_troth_02 deleted DOOR door_dwrv_load00 deleted STAT in_6th_chalk00 deleted STAT in_6th_chalk10 deleted STAT in_6th_chalk20 deleted STAT in_6th_chalk30 deleted ACTI in_lava_1024 deleted ACTI steam_lavariver deleted CONT dwrv_closet00_arms deleted STAT flora_bc_moss_19 deleted STAT flora_bc_vine_01 deleted CONT flora_bc_mushroom_04 deleted CONT flora_bc_mushroom_08 deleted STAT flora_bc_vine_05 deleted DOOR door_dwrv_loaddown00 deleted DOOR door_dwrv_loadup00 deleted STAT furn_mist512 deleted STAT ex_dwrv_ruin_tower00 deleted MISC misc_dwrv_artifact80 deleted STAT dwrv_mechhead00 deleted STAT dwrv_mechhips00 deleted ACTI blight cloud deleted LIGH blue_256_pulse_512 deleted STAT in_mold_rock_17 deleted STAT in_mold_rock_24 deleted STAT in_mud_rock_04 deleted STAT in_mud_rock_05 deleted STAT in_mud_rock_12 deleted STAT in_mud_rock_14 deleted STAT in_mud_rock_17 deleted STAT in_mud_rock_23 deleted STAT in_mud_rock_24 deleted STAT in_py_rock_02 deleted STAT in_py_rock_03 deleted STAT in_py_rock_07 deleted STAT in_py_rock_17 deleted ACTI Sound_Cave_Wind00 deleted STAT Collision Wall - INVISO!! deleted LIGH light_dwrv_neon02 deleted LIGH light_6th_brazier_01 deleted ACTI akhul_steam deleted STAT furn_6th_corprus_plate_01 deleted ACTI In_Lava_1024_01 deleted STAT In_Lava_Blacksquare deleted STAT in_sotha_lab00 deleted ACTI act_hot_oil_512 deleted STAT in_sotha_gear_chamber00 deleted LIGH light_sotha_sparks deleted ACTI active_chimney_smoke02_ovis2 deleted ACTI act_dwe_fan00 deleted ACTI Inviso_wall deleted STAT BM_IC_cavern_03 deleted STAT BM_IC_seem_01 deleted STAT in_BM_cave_28_1 deleted STAT BM_IC_cavern_03_04 deleted WEAP bm_ebonyarrow_s
these are all object records that are marked edited, and are exactly the same as the master files (I verified in the construction set), not to be confused with their references that were placed throughout. these should be deleted, since as they are exactly the same as the master file, and this project can still reference the objects from the master files' entries, and it does not in any way affect the projects' references.
Also, TESTool picked up some redundant references in a few cells:
CELL 3 7, Odrosal CELL 2 8, Dagoth Ur CELL 1 8, Red Mountain Region CELL 0 10, Vemynal CELL Akulakhan's Chamber deleted FRMR 197602, heart_akulakhan deleted FRMR 197818, in_akulakhan00 deleted FRMR 197603, in_akulacave00 deleted FRMR 197771, ex_dwrv_enter00 CELL Dagoth Ur, Facility Cavern deleted WGHT CELL Dagoth Ur, Inner Facility deleted AMBI CELL Dagoth Ur, Lower Facility deleted AMBI CELL Dagoth Ur, Outer Facility deleted AMBI CELL Odrosal, Dwemer Training Academy CELL Odrosal, Tower CELL Vemynal, Hall of Torque deleted AMBI CELL Vemynal, Outer Fortress deleted AMBI CELL -25 23, Solstheim, Hvitkald Peak deleted FRMR 7466, Terrain_rock_BM_09 deleted FRMR 7473, Terrain_rock_BM_01 CELL Dagoth Ur, Lower East Passage CELL Dagoth Ur, North Passage CELL Dagoth Ur, West Passage CELL Dagoth Ur, Lower South Tower CELL Dagoth Ur, Upper South Tower CELL Dagoth Ur, Upper Entrance CELL Dagoth Ur, North Tower CELL Dagoth Ur, Lower South Passage CELL Dagoth Ur, North Hall CELL Lost Dwemer Ruins, Sub Level CELL Dagoth Ur, Power Facility CELL Dagoth Ur, Hall of Passage CELL Forgotten Dwemer Outpost CELL Lost Dwemer Ruins, Upper level CELL Lost Dwemer Ruins, Upper Level West CELL Dagoth Ur, Tunnels CELL Akulakhan's Chamber, Tunnel CELL Dagoth Ur, Sub South Tower CELL Dagoth Ur, Mid South Tower CELL Dagoth Ur, Upper Inner Facility CELL Dagoth Ur, Power Facility Tunnel CELL Dagoth Ur, Lava Core Extraction Facility CELL Odrosal, Southeast Tower CELL Odrosal, Northwest Tower CELL Odrosal, East Corridor CELL Odrosal, Southwest Corridor CELL Odrosal, Southwest Tower CELL Odrosal, Lava Core Passage CELL Vemynal, Torque Tube Chamber CELL Vemynal, Outer Fortress Tower CELL Vemynal, Torque Tube Core CELL Vemynal, Dagoth Tunnel CELL Vemynal, Torque Tube Passage CELL Vemynal, Torque Tube Access CELL Vemynal, Torque Tube Habitation CELL Vemynal, Torque Mechanical CELL Lost Dwemer Ruins, Upper level East CELL Maze of Galom Thaneus CELL Vemynal, Torque Tube Access East CELL Lost Dwemer Ruins, Passage to Mournhold
TESTool lists all of the cells found in the plug-in, and modified a few of them.
CELL Akulakhan's Chamber deleted FRMR 197602, heart_akulakhan deleted FRMR 197818, in_akulakhan00 deleted FRMR 197603, in_akulacave00 deleted FRMR 197771, ex_dwrv_enter00 CELL -25 23, Solstheim, Hvitkald Peak deleted FRMR 7466, Terrain_rock_BM_09 deleted FRMR 7473, Terrain_rock_BM_01
TESTool reports these references [FRMR] are exactly the same as the master files'. references will get saved in this way if they are accidentally edited and undo-ed, the construction set still saves them as edited. So these should be cleaned.
CELL Dagoth Ur, Facility Cavern deleted WGHT CELL Dagoth Ur, Inner Facility deleted AMBI CELL Dagoth Ur, Lower Facility deleted AMBI CELL Dagoth Ur, Outer Facility deleted AMBICELL Vemynal, Hall of Torque deleted AMBI CELL Vemynal, Outer Fortress deleted AMBI
this reports that TESTool removed ambient light settings and water height levels that were the same as the master files. these can be deleted since there's no reason to save these unless you want these not to be edited by mods loaded eariler.
so this is what i found out, and looked into. i did clean your mod and played through it without any issues. i mainly looked into this because i like this project, but noticed that some objects kept getting reverted to old values.