So I did a reinstall. Still worked out well with the multi-boot. Maybe the trick is to do the partitioning from within OS/2, instead of the installer. So install, boot, do necessary partitioning like removing the boot manager partition.
Anyway, I did the reinstall. Got some new errors. Also it seems quite slow now, but maybe that's my imagination. The error I got was trying to install C005 fixpak. (D003 same thing). Complains about CSF_SEL.000 file. I can't find this file. The reader included with the FIX.CMD tool suggests it happens after attempting to use CSF 1.37b after 1.44, but I did it the same way as last time as far as I know. What a mess!