The Project Q cloak problem seems to affect more characters of different phenotypes than I had originally noticed. I tried changing my character's phenotype with the crafting menu customizer and noticed some fat phenotypes and some ACP phenotypes still didn't have cloak animations (I don't mean the unarmed fighting styles that don't have visible cloaks at all). Testing everything would be impractical, since Project Q has so many race-gender-phenotype combinations and so many types of animations, and I don't even know what all of them do.
But since we now know that uncompiling the models fixes these issues, I solved them in my own game by batch-uncompiling lots of files. I opened NWN Explorer, clicked open q_race.hak, right-clicked on "Models", extracted the whole folder. Then I batch-uncompiled the extracted mdl files in the directory with the command "nwnmdlcomp -d *.mdl", packed the uncompiled models into a new hak I named "q_race_ascii.hak" and gave it priority over q_race.hak in my nwnpatch.ini.
That solved all the problems with Q's cloak animations. Just to give you an example of what started working, I was testing with a human male, and if I gave him the barbarian fighting style, it had no cloak animation with the compiled Q models, but once I uncompiled them all, the barbarian style also had a working cloak animation. I should probably do the same batch-uncompiling procedure to the models in q_race2.hak, just in case. After all, I don't really know how deep the problem goes, because there are way too many different animations for different races/genders/phenotypes in Project Q, and testing them individually would be a waste of time, but uncompiling all the animation models seems to solve all the problems.
Also, I haven't been using the Q updater, so I don't know if Project Q has already fixed other animation models besides the a_da.
The window texture is simply darker. If you use a torch you'll see that it gets more orange at night. If you like I can give you some files where those windows have a self illumination.
I also had another look at the Biorural windows and fixed them too. First I extracted the entire folder of TTR models from the original game resources, uncompiled the models, did a text search for "selfillumcolor 1" in the contents of the files in the directory, and found it in four files: ttr01_s07_01.mdl, ttr01_s10_01.mdl, ttr01_t07_01.mdl, ttr01_t11_01.mdl. When I looked at the Biorural versions of the same files, they didn't have the "selfillumcolor 1 1 1" line in them, so I copy-pasted it into the same section inside those files and put my edited Biorural models into one of my own haks. Voilà , the Biorural windows now light up at night.