TextExpander was up to date, but Default Folder was not: I had 4.7.0, not the latest 4.7.1 installed. While the release notes didn't mention any of the problems I had, I'm always an outlier, and the interaction of many different systems can cause trouble. I installed 4.7.1. And the problems went away for several hours.
Then they returned.
Let's shine a light on it
I finally brought out the big guns and ran the system diagnostics. After churning away with the "extended" checkbox selected, the report was — everything was fine! Of course it was: swapping in a different computer didn't seem to improve matters.
I did some more testing with ejecting drives and swapping cables, and finally went with a distant hope. Perhaps Spotlight was the culprit. In earlier versions of OS X, I'd often seen Spotlight go nuts and drive all the cores in the CPU, spin up the fan, and wreak havoc. But according to everything I'd checked, including the simply watching disk activity lights, mdworker and other associated background processes weren't to blame.
You can disable Spotlight for specific folders or volumes by exposing the Privacy tab in the Spotlight preference pane and either dragging items or use the + to add them through a navigation dialog. I dragged my drives in, including the startup volume, and click OK to acknowledge that some programs' search feature might be disabled.
And everything got better for a while, but the hiccups continued. Everything worked fine but I still had inexplicable blurps for a moment or seconds at a time during which the rainbow spun. I purchased and tried out a Thunderbolt 2 dock which would create USB 3.0 and passthrough DisplayPort and HDMI output, thinking perhaps an internal bus or speed was an issue, but didn't realize that older Macs with USB 2.0 support won't correctly boot USB 3.0 drives over a USB 3.0 adapter! So back that went to the store.
However, it was during that final swap that something snapped: FireWire stopped working entirely. This finally provided the missing clue. Moving entirely to USB 2.0 produced a temporarily completely working system with no hiccups and no other trouble — it's just slower than I'd like. My suspicion is that the SATA controller used for the internal hard drive and the FireWire controller for two external ports is linked in some way, and some component went bad. This would explain why the internal drive stopped working correctly and FireWire external devices have also gone wonky. (It's unclear from iFixIt's teardown of this model what's in use for SATA drives.)
I decided that the Mac had to be replaced, because goodness knows what else was rattling around in there. I purchased a build-to-order replacement with 16GB — the 2014 Mac mini has soldered-on-the-board RAM, preventing user upgrades from 8GB — and when it arrived, I shut down my current system, swapped all the cables and powered up.
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