Welcome to the forums selen, and sorry to hear about issues with ranking I am sure you'd rather do without.
The best advice I can offer is that you should seek to find reputable, on-topic backlinks and citations in order to better define your site in relation to the web, it seems weaker backlink profiles are a like a house of cards that ultimately Google cannot place trust on. It's clear that Google does apply negative scoring on some backlinks but your own stronger backlink profile can make it more bullet proof.
It sounds like the non-profit you're working with would continue to exist with or without a Google and you can co-ordinate your promotion as such. It sounds like you're quite clued in to Google's guidelines and how they expect you to respond to these unnatural link warnings, and I'd suggest sticking around and looking at some recent threads on here with people having similar experiences.
Good luck in sorting it out.