I have to confess the workbench you linked wasn't created by me, but modified to run on my A1200 with Mediator PCI/Voodoo 3 (Picasso96).
Actually it was first setup by another user to run with CGX4 and BVision, he did indeed use AfA_OS to for some of these extra customisations like the transparent context-menu but I can't tell you what is needed to achieve that now. I'm using Classic Workbench 3.9 with Peterk's hlibrary for my own installs.
As has been said by NovaCoder if you have a good look at Amikit
this will give you an idea of what customisations you can add.
Most tools, etc can be downloaded from Aminet.
For Icon packs check OS4 Depot:
All the best,