A personal viewpoint, as you talk about non profit:
Some points can be met by the system, by nature build. (1,2,3,4,7,8)
however the most (learning related) COULD be implemented as kind of sub domains or iframe. (they are practically standalone frameworks, as f.e. Moodle has its own plugins, and those would not be easily integrated in a integration plugin for the system itself, as those meet specific usage themself..
There are no plugins that can do that for you. (present)
The donations part, yes there are related ones, but it will be not that easy.
Since you like to make use of plugins etc..i need to point out, that you at least should have enough knowledge to code in php and of course html/bootstrap. Else you will have to hire someone to do that for you.
Are there systems that could do all in 1 go ? : in a non profit (eg open source builds) at no extra costs, hardly none. Those that could help you with that need, will likely be af a commercial kind.
Just being honest, ( i know other cms's too) the 'wanted' items list will be tough to meet. If you are willing to pay for some, yes there
could be a solution. Out of the 'pack' most systems will only support some items, not all.