I wonder if it could be something to do specifically with USB-connected
HDD's, since my other devices work just fine? The controller in the
drive/enclosure, perhaps? I wouldn't know where to start to look there.

I tried what Toby tried as well, without success:
I had never tried actually disabling autosuspend, only unloading ehci-hcd. I 
applied the usbcore autosuspend module option to a file in modprobe.d/, rebuilt 
my initramfs, and shut down. On reboot, I tried investigating the contents of 

find /sys/ -name "autosuspend" && cat `find /sys/ -name "autosuspend"`

on my system. All reported -1, which is autosuspend off (as was set by
the usbcore module option). However, on access to my USB external hdd,
the same symptoms occur - all usb activity halts. My mouse and keyboard
fail to respond, and the machine they are connected to must be rebooted
to bring them back up - a simple rmmod/modprobe combo doesn't do the
trick to re-enable them.

If I unload the ehci-hcd module, everything is as it was before I tried
the fix. I can use my mouse, keyboard, and external hdd.

-- 
ehci_hcd module causes I/O errors in USB 2.0 devices
https://bugs.launchpad.net/bugs/88746
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