I use TiddlyWiki (http://tiddlywiki.com/) for research notes and daily work logs. At home, I track productive time (e.g., studying, reading books) using a timer, listing the amount of time devoted to each subject/book (per day) in a tab-separated file. I have not needed any sort of organizer for scheduling or for remembering good ideas.
Your workflow sounds eerily similar to how mine used to be. I'm working on Catalist (http://www.catalist.me) and would love to connect. I've built in a timer (via a Play button) to easily time your tasks so might be worth exploring.
