AFAIK, the cutscenes and CD soundtrack are the main problem (I haven't used or watched either since 2004, so I always forget about them). If not for them, the installer would more or less be:
1) "Please select your Jedi Knight directory"
2) The installer automatically has jkupd101.exe included in it, so the installer's version of JKVERSIONS (source available on Github) would legally extract JK CD 1.00 EXE from jkupd101.exe without any separate JKVersions hassle
3) The installer moves the previous JK.EXE from the directory and, in the case of Steam/GOG versions, all the extra files under a subdirectory
4) The installer's internal JKVERSIONS extracts JK CD 1.00 EXE in the JK directory. All the other files should have been reconfigured in a way that essentially the JK directory would look like it had been just installed from the disc
5) The installer extracts all the JkGfxMod (+ neural AI) files, maybe even asks you to define your preferred resolution already.
6) That should be it.
In fact, the very first prompt from the installer should be "Do you care about HD space" and then you could select the directory where the installer would extract JK CD 1.00 EXE, and it'd copy all the necessary stuff (Res2.gob, Episode folders, etc.) there - and none of the extra files.
In other words, all the things mentioned above would constitute as a self-contained installer for TODOA.
