Hi Lisa,
I was wondering the other day what had happened to you! Glad to hear you're doing better and hope you can get back to regular contributions on this forum again.
Regarding MLO and note taking...
I was actually thinking about this myself this week. My setup is getting a bit of control as I realised that I was using different apps for ideas, reminders, lists, brainstorming, research, knowledge bases, document writing, quick reference notes etc etc. In total about 12 apps across desktop and mobile! Did I say a bit out of control? The problem is the apps are all great in different ways, and keep getting better. In terms of combining with MLO, I'm in the middle of stripping out anything that isn't a pure task/project. I want MLO to be solely for clearly defined actionable activity.
Rather than recommend one particular app I would take a different tack and suggest you might think about using something with voice to text capability. This has improved massively over the last six months with Siri and Google Now becoming the tools they always promised to be. From memory, I think you were on Android, and Google Docs have recently added dictation support to make it really easy to get down longer amounts of text - via both the mobile app and via the web interface. This might be a good option if you still having periods where you are incapacitated or limited to short bursts of energy.
Graphical notes: - I'm getting boring on this front but I'll say it anyway - please look at Scapple
Digitizing hand written paper notes: has to be Evernote
Converting analogue input to digital: Surface Pro + One Note becoming unbeatable
Outline notes and lists: I've rediscovered Workflowy recently and I'm totally in love with it (i'm a sucker for elegant, simple, design)
Paper notes: Moleskine notebook + Palomino Blackwing pencil (marriage made in heaven)
Good luck and good health :-)