Definitely clean the heads, if you've put a dirty disk in chances are the heads will be dirty too and that dirt could also damage the disk as you've probably found out! I would use Kryoflux + PC drive to dump, you can clean the heads on the PC drive easier too.
I always visually inspect the surface of any disk I'm going dump by opening the shutter and rotating it slowly so I can see if there is anything on the surface, then clean it if there is! I had an 8 disk compilation recently and every disk had signs of mold on the surface so that was 16 sides to clean
Once cleaned, every disk dumped and could use Disk-Utilities to create working IPFs from the dumps!