The issue is due to OpenMW, you need to also add the two .bsa archives to your openmw.cfg (it's located in Documents\My Games\OpenMW). So it should look like this inside that config:

fallback-archive=Morrowind.bsa
fallback-archive=Tribunal.bsa
fallback-archive=Bloodmoon.bsa
fallback-archive=TR_Data.bsa
fallback-archive=PT_Data.bsa

You're welcome! Now go and make a pilgrimage to Necrom! 
And don't forget that we'll release a large update soon 

Hey, I used this same fix and it worked, i was seeing violet squares instead of some items and faces now they are restored. BUT the quality of the restored items is low as well as faces and bodies of many NPC. Playing on OpenMW. Any idea how to fix?
Thanks!

Greetings, everyone!!! First of all, thanks a lot for all that huge work done through all these years! My time to taste this wonderful travel opportunity through the fairyland of Tamriel Rebuilt has finally come. I've already been here and there, and this time I've ended up with exclamation marks at places where there Temple Domes should be. This is the first time I'm encountering such an error. Everything else shows up just right. I tried all the tips and instructions I could find over the Internet and on your Project website in particular. I tried several times to use BSAreg, WryeMash, Mlox, and maybe something else. I use stock Morrowind files within Steam folders with only cosmetic mods installed. Maybe you know a way to fix this issue, and could share it with me, please??
And also there are two problems which, I think, could be considered as bugs. Both of them cause error messages to appear at the start of the game. The text of the first one read: "Can't find 'T_SndEnv_Birds1' for region 'Vorndgad Forest Region'". I've seen that someone already mentioned that problem somewhere over the forums. The second one: "Can't find 'Mephalain Mountains' for cell 'Salien'". I believe there's a typo in the word "Mephalain", and that's the cause :)
Anyway, the latter two problems don't do anything nasty to my experience, but the first one really does and breaks the game's atmosphere thoroughly.

Thank you very much in advance!!!
Aquelyra

Yay!!! I did it!!!! You need to rename files "tr_flora_templedome_01.nif" and "tr_flora_templedome_02.nif" from the archive "T_D_v7_Hotfix\tr - meshes (high and low)\o" (this archive is available at the address I mentioned in the message above) into "tr_flora_amanita_01.nif" and "tr_flora_amanita_02.nif" respectively and put them into your folder ...\Morrowind\Data Files\Meshes\TR\f. Whew...
The one problem remains, with "Mephalain" and "Sailen" one, and I think it's impossible to resolve it without a deep understanding of how to create, pack and unpack mods, etc. It doesn't affect my experience yet.
Now I have another problem to solve. There are two types of trees that appear correctly only while being near them: "Flora_tree_MH_01" and "Flora_tree_MH_02". Let's see what Google can say about it

Thanks a lot for your reply!!! My Tamriel Data has version 7.1.7. I guess it's the latest one.
I use graphic herbalism, so that was the only way to resolve the problem with mushrooms because Google says this is a known problem with the aforementioned mod and it awaits its update in the "near future".

Hi there!!! You flatter me with your attention, outlander, much appreciate it!!

That was an outdated version of Skyrim: Home of the Nords.

I had decided to get rid of this Skyrim mod, but the problem remained. After I renamed the file, everything became just fine.

That is an error caused by some outdated third party plugin for Tamriel Rebuilt or you are loading TR_Mainland before Tamriel_Data (but you should have more issues that way).

I use a program called "mlox" to sort my plugins correctly. But yes, it's all about an outdated plugin "MCA - TR addon", just noticed it . I tried to patch it with "TR_FilePatcher" but, alas, no luck. I think I'm fine with that... Because this plugin makes Morrowind alive for real.
The same problem occurred with the TR addon for "Abot's Window Glow" (like "object reference 'in_mh_window_01n' missing in master file...) after I tried to find a solution for all these aforementioned problems. I don't know what did I do wrong. But now I'm going to try another mod for that: "Windows Glow in the Dahrk". What a tasty name
"Book rotate" became a pain too, but that's another story...
Thanks again!!!

But yes, it's all about an outdated plugin "MCA - TR addon", just noticed it .

The bane of many people's installations. It's a shame that is permissions do not allow for updates.

Glow in the Dahrk is the future (which we are living in), so good choice moving to that.

For broken textures, I used an archive with upscaled vanilla textures found somewhere on Nexus Mods. Maybe that would help you too.

I installed TR through nexus. TR data, registered BSAs. Morrowind comes alive and Morrowind reborn both work, as do my shade enhancer, script extender, yada yada. Everything seems to be done correctly, however none of the boatmen offer trips to the mainland, and if I swim there, I get error messages about missing meshes/textures. 

Can anyone help me use process of elimination to figure out what's wrong. This game got me through a very rough childhood, and now that I have the time and money to play a modded version of it, I'm ravenously trying to experience Morrowind anew and TR is a cornerstone of that temple.

Hope for a speedy reply, thanks guys!

I see that it is a meshing/image issue between MR and TR. The patch is outdated, so I'm going to delete the meshes from the MR file and see if that will fix the issue.

The 3.0 compatability patch works well enough. lol I am suddenly missing an NPC. TR_m0_Sentius_Veros

And the meshes \f\furn_rug but it seems I can fix that with a name change. And meshes\x\ex_imp_lighthouse which I will probably just delete.

Seems I'll get the mods working together well enough, Wish me luck. Love the mod!

Thank you for the response! I do not use OpenMW. My BSAs are as following: 
[Archives]
Archive 0=Tribunal.bsa
Archive 1=Bloodmoon.bsa
Archive 2=PT_Data.bsa
Archive 3=TR_Data.bsa

I have attempted to use MR and TR by themselves, and the game hard crashes as I approach the mainland. I have attempted to use the MR 3.0 patch and TR, and the missing items namely the boatswain, a ballista, and a lighthouse. Last night the game did not crash, however when I traveled back to Balmora the canals were missing an item. I would get the occasional missing item warning but it was playable if not a bit unwieldy. I tried getting rid of MR and using other mods to flesh out the mainland, it didn't work so I went back to MR but now the game hard crashes when it tells me the lighthouse is missing, an issue I did not have before.

It seems like I'd need to load an older TR to make it run with MR. Every compatibility patch I've seen is a few years old when TR was smaller. 

The missing textures were from MR, not TR. But after I fixed that issue it seems to have become inconsistencies between the TR and MR folders. Either missing/old/corrupted files or the program is confusing which packet goes where. The issue isn't specifically with your wonderful, wonderful mod. It's a compatibility bug that I am obsessed with fixing. Is there a log where I could download an older TR that will work with MR or MSGO (Seems MSGO can fix the compatibility issues when it was relevant.) Or, perhaps I could cherrypick from the MR mod to sprinkle Vvardenfell with extra content? I don't expect help with issues that aren't specifically because of your mod, just pointed in the right direction, which is "Am I about to spend ten hours trying to handcraft mods when the programs do not work that way?"

At this point Morrowind Rebirth is the issue, TR works completely fine other than it makes MR break. I'll just have to will it into working somehow.

I have them tentatively working together, good enough for me. Time to get my Morrowind on!

Thank you!