Then that click-click sector is a bad sector. It needs to be mapped in the bad table. Not sure how you can do that with Mac software, but I know you can do that with PC software. Once all known bad cylinders are stored in the preformatted bad table, that blocks them off from OS tools being able to use it. Then the drive will skip over that sector every time.
Woo, worked out the graphics issue - the monitor didn't like been overclocked that hard from the IIx. It is usually ok at 75hz, but for some reason it wasn't here.
At the moment I've found that it runs at 72hz in 800x600... still technically too fast, but the screen copes.
Just disk and possibly pram issues now! So close! From dead to photoshop in ~3 weeks!
Right now it's the original 21-ish MiB of the original drive, which gives 18MiB formatted. The size is hard coded in the ROMs, and there's no option to specify the number of cylinders/heads in the HyperDrive software. AFAIK there was no way to discover the size of a drive with the ST-506 interface either, so, you'd be stuck with whatever size the board was made for.