How to efficiently organize my PhD data, papers and notes?
I'll take on a rather technical side and talk from my experience.

Folder hierarchy

I start a folder for each "project", which is either a separate talk, an idea, a paper, etc. (Funnily, I store code elsewhere. Same with large research data.)

Previously, I put literature from the related literature research in a subfolder of a "project", nowadays I just push papers in a magically-syncing-around folder. I am sure, there are better solutions though. Zotero? Papers? That's a separate question, actually. But same software would also manage the citation database for you.

In the same "project" folder the template files for the paper land: publishers often prescribe the looks and style of a paper. Typically in the root of a "project", paper sources lie, under version control. Nowadays this spells git. I've been checking images into git, too. There are better ways now, with git lfs or git annex, but that's again too specific. (By the way, revisions of a paper for a resubmission elsewhere become branches in git.)

The key thing: at some point I had a further "project", the thesis. I made subfolders for each chapter (that roughly corresponded to the papers). I already had text to put there. These subfolders had further subfolders for images, which I hardlinked from their respective projects.

Large data

Zenodo is wonderful for storage of the final large data.

For development, we had an FTP server and OwnCloud to share data in the research group and to allow for upload by partners and subcontractors.

I found git annex to be both useful and a huge pain in the ass for this. So test it beforehand, and your milage may vary.

Definitely invest in a backup solution. Nothing is more irritating than loosing research data. That's again a separate question, but both proper storage (RAID or something) and proper backuping (RAID won't help, if a thunderbold grills your PC) are important.

Byline

Typically a research group has some kind of data sharing and collaboration platform running. Go with it. If not: it's rather a software / eGroupware question.

Always do a fresh backup.