Markdown files and Logseq https://logseq.com/ as the front end. I’ve been using Mardown for over 10 years, and it’s worked for me. Work uses JIRA, but I keep my own notes and copy in them in as necessary.

I just use dd. It can take days, but it’s worth it.

I’ve used these kinds of disks in my NAS at least since 2017 with no issues. Just test thoroughly before using. I usually do SMART short and long tests, and then a bit by bit write and read of the entire disk. I’ve caught a couple that failed right away. If it passes that, then it’s usually good for years.