Q: System wont boot after OS X 10.11.2 update

My initial setup: a 250GB AirBook which already had 10.11, with about 200GB on it; regular TimeCapsule backups; and a 1TB external drive (FireWire 800 connection) divided into 4 equal 250GB volumes - 1 each for bootable clones (made with SuperDuper) of my AB (usually made about weekly) and my wife’s (same Mac, somewhat different SW), 2 more for different kinds of extras (neither of which has much on it).

Since I lost all my data twice long ago, I’ve become a belt-and-suspenders user. Not only do I have 2 BU’s (TC and my clone), I also have TechTool Pro, which makes an “eDrive”, a small bootable partition on my AirBook from which I can run TTP; and a bootable USB of DiskWarrior (which is also on my AB).

1. Make fresh clone of AB to “AB Clone” (ABC)
2. transfer the stuff from one of the “extras” volume to the other, so as to have yet another 250GB volume free, which I formatted and named ElCap (EC).
3. Install 10.11.2 on EC, make sure it boots (it most likely will, mine did)
4. booted up from EC, used Migration assistant to migrate only the system settings, and the documents and data (the 2nd and 3rd choices you’re offered), but none of the apps, from my AB to ElCap. Rebooted a couple of times, to make sure it was OK.
5. (Ah, yes, now it turns out I used 2 external volumes!) Booted up from EC, DL’d and installed SuperDuper! on it, made sure it booted with that.
6. Booted from EC, I cloned that to ABC (using SD’s “Erase then copy” option).
7. Booted from ABC, to make sure it was OK.
8. Booted from EC, I started to repopulate my apps by DL’ing and re-installing them, according to the theory I described above, starting with the most essential. (Copy and paste or drag and drop won’t work for me here, because most apps install arcane things throughout the system which I don’t know about).
9. After every few installs I’d see if EC booted up, and if it did, I cloned it to ABC (this time using SD’s “smart update” function, which only copies changed items, and is thus much faster than “erase then copy”).
10. Every few times, for safety’s sake, I tried booting from ABC. Also, every now and then I booted from the AB, from where I ran DW on both EC and ABC, to make sure the directory was OK (occasionally it found something to repair, but I never had a problem in this regard).
11. Somewhere toward the end I installed that Kensington trackball driver, which hung my system (that was the BAM).
12. Booted into AB (but it might have been ABC), and opened up EC, and hunted down the trackball driver and its .kext (*), and deleted them (and emptied the trash).
13. EC now booted fine, so I installed everything else I wanted - omitting the Kensigton driver, of course - until I was done. I encountered no more problems.
14. Finally, I cloned ABC to AB (“erase then copy”).

*  I don’t remember any more for sure where I found the files. But the trackball driver is a pref pane, and .kext files are kernel extensions, and thus in an Extensions folder. Both are in Computer>My AirBook>Library, then >Extensions, and >PreferencePanes. That said, there’s a strange thing about .kexts: I read that they’re ony functional if the related app is active, or trying to be, otherwise they just fill space (but they’re small). So, despite also reading that not only the app, but its kext must always be removed, which I did, I’m not sure it’s really necessary.

In retrospect, though, I could have saved the time I spent hunting, and it would have been safer, had I done it differently, not as in 12 (above). Still, the way I did it pretty much proved the culprit. Instead, though, I could have done this, which I recommend, since then you don’t have to hunt anything down to throw out:

12. Boot into AB, clone ABC to EC (“erase then copy”), and go on installing apps, omitting, of course, the Kensington driver.

Two more things:

First, I had a few games, which use Steam. Feeling no great need for them, a bit wary of that installation (perhaps needlessly), and tired of fooling with my Mac for now, I haven’t re-installed that yet. But I will, sooner or later, and then I’ll see.

Second: There might be an easier way to do all this using something like CleanMyMac, installed on a functional clone, (which plays well with El Capitan) to delete all the things which you suspect might be problematic (or, conversely, delete everything except for “sure things”), reboot, and, if you got the right files, the update via the App Store to 10.11.2 should go fine. But that’s another story, which I never played.

Good luck! And be prepared to not see your family or friends, or use your Mac for many, many hours! Get a good book to read while the time-consuming stuff is going on.

Uahu! That's a piece of work.

Thanks for dedicating so much of your time, I will learn it well and then make a trial.

In parallel, still pursuing your idea that isolating the culprit(s) app(s) solves the problem, I thought to use a short cut: find and delete "suspicious" apps before upgrading to 10.11.2.

As a help for finding "suspects", I checked that Roaring Apps site mentioned by linda2009. Also dedicated some thought to apps that are behaving odd since installing El Capitan, like your TrackBall.

Roaring Apps has very few apps tested for 10.11 but for Yosemite or Maverick some apps that I have installed are red: Photoshop Elements 9, Parallels 7 and Viber (redundant anyway, don't use it). Perhaps for El Capitan these apps might be red as well?

Checked with Parallels website: they issued a warning that Parallels 7 will not work with El Capitan (in fact, it already made me problems with Yosemite and Maverick).

And Elements (like your Trackball) is behaving very odd since 10.11 installation.

Both are very suspicious indeed !

Thanks again for your help.

Something else occurred to me, which may add several layers of complexity. It may be that some apps individually play nice with El Cap, but don't play nice with one another - or even two or three others in a bunch. That would make it nearly impossible for normal civilians to sort out, and would account for some of the bugs in the first or second iterations of the software we get.

Re the RoaringApps site: the guy has done a very helpful piece of work, but, as he says, he didn't do all that testing himself. He relies on reports, which may or may not be reliable or up-to-date. That means that the verdict on the list is probably a good guide, but may not be accepted blindly; checking the apps individually lets you know how many reports he's gathered, and the more reports the more reliable the assessment. Case in point, the faulty Kensington driver I found. It turns out that his report of this was a bit misleading (but not his fault), because it was based on a user's experience with it on an earlier OS - which I only found out just now; I, too, know it worked fine back then. So the more research you do on his site, the more you know how to proceed.