This is trivial in org mode. There are multiple ways to do this. The simplest is:
Put your TODOs in the order you want. You can easily reorder them using Alt + Up or Alt + Down. Marking it as complete is also trivial.
The canonical way to do this is to make each TODO a headline with the TODO keyword. To mark as done, put your cursor on the headline and press Shift-Right.
Alternatively, you can use checklists and just press C-c C-c to mark an item as done:
- [ ] Fix widget
- [X] Extend Screen
- [ ] Profit
But you'll find doing it via headlines works best with the rest of org mode (e.g. you can perform queries on headlines, but not on lists).
> Once there are too many completed tasks at the top, I move them down into a "Done" section.
You can refile any headline to another section. Org mode also has the concept of archiving a headline. By default it moves it to an archive file, but I'm sure the location can be customized.
> linking tasks to further notes would be great to have
Org mode supports links - you can link to about anything - another file, another section in the same file, a line number in a file, a search string, an image, a PDF, a web site, etc.
In practice, if you use the headline version of TODO, you just keep the relevant notes under that headline. You can collapse all headlines if you just want to see the TODOs, and expand any given headline to see the details. But even if you go the checklist route you can just add a link to detailed notes.
You can learn to do all this in Org mode in under 30 minutes, if you find the right tutorial/video.
> without explicitly setting due dates or priority "scores"
These are entirely optional in org mode and not on by default.
If you want to be able to add a TODO in the right spot without moving your cursor to the exact location, you'll want to learn about capture templates, which is a bit more advanced.