Unchecked 32-bit mode. Everything else in System Preferences appears to be OK apart from the Network pane. What sort of things would cause this issue?
Glad you got your issue resolved. Cory is definitely an expert at quite a few things!
As for any causes of the issues you had, that could depend on a number of factors. As it is, you did make a huge jump from Mountain Lion to El Capitan. Did you just take the upgrade path? Myself, when I moved from Yosemite to El Capitan (not as huge an upgrade as you did), after (of course) making a SuperDuper! backup to an external device (actually two external drives), along with insuring that my 5 critical apps each had the necessary upgrade for El Capitan compatibility, I erased and formatted my internal drive first (I have SSDs inside each of my Macs), then did a clean installation of OS 10.11.1 (yes, not the initial release of El Capitan, and I had my reasons), and then used Migration Assistant to "migrate"/copy all the necessary "stuff" from my backup. That process, for both of my machines, went very well.
Of course, I am very "anal" when it comes to disk cleanup/maintenance/repairs (hardly ever need to do repairs), as I tend to keep my Macs "lean and clean". For your situation, it could be difficult to try and pinpoint why you encountered issues. I wish I could be of more help. Maybe Cory can chime in and offer some expert opinions.
One other thing: what version of El Capitan are you using? Version 10.11.3 came out over a month ago, and if you need it, you can get the OS 10.11.3 Combo Updater from here:
https://support.apple.com/kb/DL1859?locale=en_US
Make a backup first, though, before applying it, just in case. And, OS 10.11.4 has been in beta testing for quite a while, and I recently read that Apple plans on releasing the final version around March 15th.