First, please explain what you mean by "the clean install I was forced into (after OSX virtually had frozen) was from Apple online". I have never been forced into a clean installation!
Secondly, my experience with OS 10.11.2 is just the opposite of yours! The main thing I noticed is that starting up and shutting down are faster. That was one of my complaints with OS 10.11.1, especially compared to the last version of Yosemite, 10.10.5. Not really noticed any other speed improvements, but nothing is slower than it was with OS 10.11.1.
Third, I do not use Apple Mail, as I prefer Outlook. Outlook is functioning fine (as are Word and Excel). Maybe someone else can provide more advice regarding Apple's Mail software.
It's good that you are making backups. What you could do is the following:
1. Download and install the excellent freeware program Onyx to Repair Permissions, In case you don't know, that function is no longer available in El Capitan, as (supposedly) Os 10.11.x takes care of that. But, I run Onyx on both of my machines every Saturday as part of my disk cleanup/maintenance/repair (repairs are, thankfully, rarely ever needed to be done) processing, and Onyx certainly does Repair Permissions. You can get the El Capitan version of Onyx from here:
http://www.titanium.free.fr/onyx.html
You'll want to get Version 3.1.2, unless Version 3.3.3 is out of beta testing, and has been released.
Onyx has some other cleanup features that are beneficial to run.
2. Boot to the (hidden) Recovery Partition, and run Disk Utility from there to 1) Verify and Repair your internal drive at the top (ie, Volume) level, and Verify and Repair the disk at the second (ie, Partition) level. This link describes how to boot to that partition, and what it contains:
https://support.apple.com/en-us/HT201314
3. If none of that helps you much, note that via the Recovery Partition, you can Erase and Format (and if necessary, Partition) your internal drive, and then do a fresh installation of OS 10.11.2. Then, you can boot up your iMac and use Migration Assistant to "migrate"/copy all the non-system stuff from your Time Machine backup.