How do I find out what mod is removing a vanilla item?

I have a large collection of mods together. And I'm seeing errors like:

Object reference "in_c_door_arched"
missing in master file.
Unable to find referenced object "Rararyn Radarys" in script raz_balmora_attack_script.

Both of those exist in the vanilla game. If I load the relevant individual mod and the masters, I have no problems. But when I run my large collection of mods together, something seems to be deleting the vanilla item, or renaming it.

Download http://planetelderscrolls.gamespy.com/View.php?view=utilities.detail&id=34, and place the .exe in your morrowind root directory. Launch it, select "Generate detailed conflict report", and select "execute". This will output a conflict report of all of the mods you have in your load order. Warning: you will probably generate a lot of conflicts; this is normal if you have a large mod set and several .esps edit the same objects (because Morrowind is just going to load the last version of that object edited by an .esp in date order anyway).

Open up the output file (if one is generated, otherwise just Ctrl+A, Ctrl+C the execution log and paste into a .txt file), and do a Ctrl+F and search for the object IDs that you're having issues with. It should probably reveal what the problem is. (And if you read the rest of your conflict report, you might discover some other issues that you weren't aware of!)

Good luck!

TES Tool has crashed every single time I've tried to do a conflict report.

I may be running too many mods.

Curious. I see quite a few of those as well, however the reason behind it is different.

I've noted while programming SmartMerger that those errors tend to pop up when the object isn't included in the plugin. Reason behind it is the plugin SHOULD contain everything you need to create or use the plugin effectively, minus what's in the master files. (That's why in recent versions of SmartMerger forcibly keeps all land textures that are required for extracted lands and whatnot).

At the off chance that an item is actually deleted in a mod you could use SmartMerger to find them for you. ie: --query "*;1(dele)" should do the job, (although might get away with just "*;dele" too.), although if you have to merge them all first I am not so certain. I would suggest rather a batch and have it load them all individually and spill the results. If you use a Bash shell I can easily supply a workable script. If not, a list of the plugins you use and I could generate a batch file compatible for MS-DOS that you just save and execute (and wait). If you have to end up merging use --no_dialog_merge and --no_output this will speed up the process since you aren't saving an output.