How do I reinstall Yosemite while keeping my personal files & settings?

Hi,
I am running Yosemite (10.10.2) on my 2013 Macbook Air and its in need of some love. Most notably, my Notes app has broken (it crashes on every attempt to open it) and my bluetooth has gone haywire (device detection and personal hotspot works when they feel like it), my display will randomly go black and is becoming an increasingly mysterious and lengthy process to get it back (normally just mashing keys and opening and closing the lid several times over). Thats just the half of it.
I want to say the mass majority of these issues began after signing myself up to receive all these alpha, beta, omega, apple tree pre-seed, under-cooked releases or whatever apple pushes down the pipeline. Needless to say, I feel its time to reinstall my OS though I am quickly discovering that this whole process was significantly easier in a Windows environment which seems really counter-intuitive considering well, this is Apple and things are just supposed to work like magical butter.
So I ended up reinstalling Yosemite through the Recovery Utility (CMD+R). It downloaded from the internet and installed. My personal files were kept intact but it didn't fix my Notes app as it still kept quitting unexpectedly when trying to launch it. So I opted to perform a clean install. I quickly realized this was a TERRIBLE idea as I was unable to recover important settings like my keychain passwords, my email accounts and so forth. Thankfully I made a time machine backup before attempting any of this so I am right back where I started (sort of).
I need some help please.
My goal is to perform a clean install of Yosemite to rid myself of these OS oddities meanwhile keeping everything important. This includes, most notably:
my personal document, photo and music files
my iTunes library
my iPhoto library (and more importantly, the settings, albums tags, image edits etc etc) that I've made over the years
my keychain passwords
my email accounts (it took me almost an hour to setup and properly configure all 9 of my email accounts and i don't want to go through that again)
my calendar and events within it
Other settings I would like to keep, but am willing to sacrifice are:
my iMessage history
my applications
my user experience settings; things like the dock size and behaviour, track pad scroll speed etc etc etc. I'm on the fence with this one since I've plugged in so much sudo code into terminal trying to accomplish things in the past, that I fear theres some settings that shouldn't be restored.
So Apple community, what say thee; what is my best course of action?
Thank you,
-Brendon

Oh boy... throughout all of this i think I've really done a number. In trying to execute the instructions in the link you provided, I receive this error while trying to access my internet accounts panel under system preferences:
"Preferences Error
Could not load Internet Accounts preference pane."
What have I done lol...

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How do I reinstall Yosemite while keeping my personal files & settings?

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