The HDD is recognized when I boot from the 3.1 workbench disk hence why I can modify the S: files with Ed, but I can't load into 3.9 as all attempts have been unsuccessful.
But have you done something with the WBStartup drawer on the 3.9 HD? Either rename it so the LoadWB command can't find it, or delete everything inside it. Also try deleting the Prefs/Env-Archive/Sys/wbpattern.prefs file in order to prevent the Amiga from using precious RAM on any backdrops.
Regarding the standard version of HDToolBox on the Install3.1 disk, have in mind that it can't be used directly with CF cards since it needs to be patched first.
Maybe one of my ready-made Amiga911 boot disks could be of interest? This one should be suitable for you:
https://www.box.com/s/30snom1sogojovgvfretIt has everything needed for setting up a harddisk (including patched HDToolBox), and it also have the required files for using CF cards via PCMCIA. It is also possible to install Workbench directly from ADF image files after booting the Amiga911 disk. This rather amateurish video shows how it can be done:
http://www.youtube.com/watch?v=gtRTs2ea1d0&feature=share&list=PLhAsZHVD_BhG1Va0RX80N6HGetw9tc6hDJust have in mind that some files has to be copied from the Workbench disk upon booting it for the very first time.
You can read more about the Amiga911 disk here:
http://amiga911maker.site11.com
