Managed to get this system to Sierra from ElCap.6 on the second try, by booting the installer normally.
For groundwork, I updated Clover to 3751 and copied FakeSMC.kext and AtherosE2200Ethernet.kext to /EFI/EFI/CLOVER/kexts/other, previously occupied by Shiki.kext and iMac,kext (a plist-only module to inject device IDs for Shiki and the GTX960). I was already running on an iMac 14,2 sysdef.
Installer app ran very quickly. Rebooted, added nv_disable=1, selected installer, selected "without caches" and booted. Apple logo comes up, row of pluses in the top left. Progress bar goes maybe a tenth. Pinwheel, mouse works. Does nothing for about 10-15 minutes, then freezes, necessitating a hard reset.
ElCap was unaffected, and still booted. The installer was still available in Clover. After going back into ElCap to make sure it worked, I tried the installer again, but booting it normally (I think I saw someone on this thread try that). It went through the Apple logo, into the GUI and installed. I went through the post-install clean-up of installing nvidia drivers and adjusting Clover accordingly. This was a bit difficult as Clover Configurator wouldn't mount the EFI partition and I needed to use Terminal to do it. It turned out that the drives occasionally trade places and at the time my macOS drive was disk1, swapping back to disk0 a couple of reboots later just to keep me on my toes. No effect on Windows so far. It took a couple of runs of Clover-ALC120 to get sound back, and the system was back up and running.
And it still seems okay, though I had to turn off sleep tonight after I interrupted a sleep attempt and effectively locked it, forcing a hard reset. Siri works, Shiki plays iTunes Store content, all appears well, but will play some more this weekend.