After review of the save i can answer some of your issues.
Voodoo Initiation and demonic sacrifices are blocked because a certain event prerequisite will never fire on lowest difficulty. Nearly everything voodoo related is disabled on lowest difficulty by the is lockout.
Not sure whats going on with protegee and the message.
That said your only a few VIPs away from being able to start making the final craft for a win. Acquire a Cardinal(church bases, shrine ships, or bought), A guild-master(Traders bases, very large trader ships like battleships, or bought), Academy provost(base, large ships, or bought) And either a Public enemy(found rarely on the smuggler ship that is a Millennium Falcon expy) or A stargod coordinator(Silver towers or bases). Lastly a Belter(From space freighters, or as a get one free from broken smuggler negotiators(which can be found by progressing the city arc after terminal terror mission) After that you can do the end game.
I'll just start the game from the beginning then on second difficulty, then. I am really grateful you took your time to help me. Cheers.
Edit: Oh, and, before someone Molotovs on my house, I play on easiest difficulty, because I always played X-Com on lowest, since I was a kid that did not know English, but I still wanted to play TFTD (I did not like EU). I also do all sorts of self imposing challenges, like no equipment/weapons/craft I can't make myself, no slave soldiers, just 3 bases, no explosive weapons, etc. so I get enough fun and challenge as it is. I don't need bragging rights for being hard-core.