Circa

There really isn't going to be another way around it, you need OpenJK or JAEnhanced or some other derivative of it. The error is due to the models hitting limits that the base game has set. OpenJK raises those limits.
The only other way is to manually decrease the model's triangle count in a program like Blender but that sounds easier than it is. I forget the function name in Blender but there is a button to do it but it is destructive and can result in bad looking results if you aren't familiar enough with it.
You're probably better off further troubleshooting why your computer isn't letting you run OpenJK, I've never heard of that happening before and may be a concerning broader issue.

The saber builder is kind of a bonus feature and only works currently with the parts that it has. You have to select the "Saber Builder" saber in the list. You won't be able to use parts from the other lightsabers right now. In future versions that may be an option if someone makes it work but right now it is limited.
The cheat menu is in the pause menu.

Most server trackers filter them out (GameTracker and ParaTracker included) or just show them as a period.
I remember having trouble with this too, though my my main OS is macOS and I found I was only able to save it properly on there. As soon as I'd open and save it on Windows it wouldn't work.
Here's a .cfg with the character and correct encoding, try pasting the rest of your current cfg into this one and saving with Notepad++ or something similar. (taken straight from my server's server.cfg that is working right now on the server list)
https://rvn.im/files/o/server_specialchar.zip

Sorry I didn't look that closely at it since I assumed Cerez had tested before uploading. I just included the missing strings file that is required for SP menu support. I also went ahead and just included all of the original files too so you only need one pk3 for SP. If you click the download link on the main download page it will show two downloads, original and the new SP one.
By the way, if you wanted to learn for yourself how to edit these things or make your own mods, a good starting place is this tutorial which links to other tutorials on various topics. The tutorial for SP support can be found here and here.

Before you ask questions, I recommend looking through the tutorial section. Specifically this page & RichDiesal's old website, where he goes through all of the very basics. Sounds are covered in the Entities section:
https://jkhub.org/mapping/richdiesal/richdiesal.htm
Many mappers these days have moved on from GTKRadiant to the newer NetRadiant-Custom (NRC for short). This tutorial on the MovieBattles wiki is quite in depth.
https://jkhub.org/tutorials/mapping/netradiant-custom-mapping-tutorial-series-r216/
As far as the game's maps you can find those and other source files in this section.

Take a look at these tutorials. RGB textures need alpha channels and saved a certain way. However in my experience I've had trouble doing this properly in modern versions of Photoshop for some reason.
 

Gravity can be set in the map's wordspawn entity, yes. You can learn how to do simple entity modding here and here.
Also, you are correct on afi's syntax being off. He should have put bind space "+moveup;g_gravity 300"

Most other Darth Vader NPCs that people have made do this with the lightsaber hum looping sound. Maybe someone else knows of a better way but I think this may be the way to go.
 

I used this tutorial for my Christmas map, although it was for MP, it should work for SP too I assume. Wonko is right, NPC_Target activates on death so no need for an additional script.
http://map-forge.net/wiki/doku.php?id=tutorials:npcwaves_data:npcwaves
Of course this isn't multiple waves in your case, but it shows you how to use the counter function so a script runs when all NPCs are dead that are linked to the counter, even if its just 2.

Is the mod you're talking about this one?
https://community.pcgamingwiki.com/files/file/1190-mati-hootis-assorted-fixes-for-jedi-academy/
Looks like all menu changes. The red saber option should already be an option with JAEnhanced with the RGB option.
Projected shadows is just cg_shadows 3 in the console.
Subtitles for all voiceovers is already in the JAenhanced menu.
The menu music can easily be changed. If you'd like that menu music I can change that for you for JAEnhanced or you can do it yourself. Open zZz_jaenhanced.pk3 and go to the ui folder, then main.menu, open with Notepad. Control + F to search for music. Change the below line.
exec "music music/yavin2_old/yavtemp_explore" ; Replace it with this:
exec "music music/mp/MP_action4" ;  

Yes, though it is not a very smooth transition right now which is probably why it isn't default. You'll need to put this command in the console:
cg_trueinvertsaber 1
I have no idea why the command is called that but it should do what you want, just with a slight stutter between switching from a weapon to the saber.

That is my personal model I made for myself. I hadn’t planned on releasing it but I won’t say I never will I suppose. 

Without editing the mod itself, you can use commands that work like so:
 
 
Or you can learn to edit the mod to put it in the menu with tutorials like this:
 
 

Should just be a matter of changing the frame number in animations.cfg in models/players/_humanoid for each stance to match the frame number of the strong style. Just did it in about 2 minutes here for you.
https://circa.im/files/jka/strongstance.pk3

Your screenshots show your folders aren’t set up the way I listed in my above post. You have 2 extra folders that aren’t needed, the jaenhanced folder goes directly in gamedata. Do not use the “Windows” or “Windows 32bit” folders.

If you're using an old version of the plugin, then yes. The link to the most recent version is in that thread I linked.
For the alpha channel shader, it should look like this I believe (path to texture is placeholder):
 
models/players/person/texture_alpha { cull disable { map models/players/person/texture_alpha alphaFunc GE128 blendFunc GL_SRC_ALPHA GL_ONE_MINUS_SRC_ALPHA depthWrite rgbGen lightingDiffuse } }  

Nothing should go in base unless you plan on playing the base game. If you're only going to be playin JAEnhanced, your other pk3s can go in the jaenhanced folder, although it does load pk3s from both, it does not load DLLs from both.
The folder structure in the ZIP file is how it should be in your GameData alongside the base folder. The readme says to drop everything in GameData and that should be all you need to do.

 
Not sure what else to tell you, other than make sure your graphics drivers are up to date. Maybe try launching the .exe as administrator.
You should try going to Documents/My Games/jaenhanced and deleting the files in there as well, its possible you had a weird graphics setting causing it.

In simpler terms, you have to edit the source code to raise such limits. OpenJK and its various forks already raise them a decent amount.
Also like you said, there are a lot of Boba models out there that look really good already. Verts and polys will only get you so far before you need to also have a modern renderer to make it look worth using. There's a reason modelers still optimize their high res models to work in JKA properly. They still look great, just not as great as they would in a modern game with a modern engine and renderer like Battlefront II.
It's best to aim for OpenJK's limits at the most. You could also look into making it compatible with rend2, which is an experimental modern renderer that can be used with OpenJK.

JAEnhanced has this feature. Release should be out this week sometime.
 

You can just use commands for this, but if its a skin with a lot of different versions you may need to open up the PK3 file to see what each .skin file is named.
Here's a tutorial on the commands:
The other way is to modify the mod itself so the skin shows up in the menu. You can learn how to do that with this tutorial:
 

That usually means Radiant isn't pointing to the right base folder for the textures. Do all the shaders show in the shader browser?

Okay, I finished Leela Jedi. I have to say, this model is kind of terrible by today's standards. It's weighted terribly. I made icons for the parts in the menu and fixed the JK2-isms so it works with JKA as best as it can.
 
https://circa.im/files/jka/leela_jedi_SP.pk3
 
I'm not sure I want to do the Civilian one, simply because it has a lot more parts to deal with and it'd take a lot more time.
 
Kind of unrelated, but I highly recommend using Scerendo's female customization instead of this. He used parts of the Leela model but made them a lot better.

I discovered/remembered the issue. It's an easy fix but if you ever want to use a custom animation mod, it will have to be fixed in that mod as well. Here's a pk3 to fix the issue:
 
https://circa.im/files/jka/walk_fix.zip
 
Open the zip, copy the pk3, paste it in your base folder.

I assume you mean like in real life, how doors swing open?
 
There should be a func_door_rotate that you'd use instead of func_door. But I'm not positive. 
 
EDIT: Szico actually made a tutorial.  @@GPChannel
 
https://jkhub.org/topic/10098-rotating-doors/

The game loads PK3 files in alphabetical order, which means the asset0-3.pk3 files are loaded first, and anything that comes after that alphabetically are loaded after, and overwrite anything that is the same in the previous files. So if you have a mod that changes the skin of Tavion in a pk3 called aSkinOfTavion.pk3, it wouldn't overwrite anything because the assets are being loaded after it, thus overwriting the pk3.
 
So, many people put the letter Z in their file name so it is loaded either last or as far down the list as possible, ensuring there are no conflicts with other mods that may change something theirs does.
 
In my opinion, its a bad habit to get into. You should only put Z's in your file name if you know its going to cause issues with other common PK3s. Otherwise you should just name it something normal, and let the user put Z's on it if they need to. I like to keep my base folder as organized as possible, and I make sure only the pk3s with Z's are the ones that need it. Otherwise it just makes it harder to find things.