When I found that Partition Wizard did not work, I decided to wait to see if a fix appeared. After a few months, I decided that the block read errors and slow speed was too much to bear and ordered a SII 3114 card and a SATA HDD and DVD Writer. While waiting, I thought I would see what I could do with the parallel card.
Workbench was already on SFS, but I changed my Backup partition on a second drive to SFS2. I also bumped the two hard drives from 'Best PIO' to UDMA 6 (I had nothing to lose since I was getting Read errors, anyway). I also printed out the IDE documentation ready for the new SII card.
I found that the Workbench blocksize was 2048 instead of 512 and the docs said that was a no-no. I put it right and copied from the backup to Workbench.
The speed is impressive. Backups, even on the latest FFS partitions are very quick.
Now, the question. The docs make it clear that the FLUSH_CACHE issue might have been part of the problem (the drives are old). The docs also make it clear that SFS might not actually report any problems it might see and that it is better to use the diskcache.library with SFS. A bit of Googling suggested that it might be one of the Kickstart modules. Kicklayout includes a diskcache.library..kmod call and the module is also present. Is this enough to get disk-caching with SFS 2 or is there more to do?