Hey, I'm making right now the same than you, but I'm starting from the Lite version; I want to add the dock.
First I've copied the Dock of the WBstartup, and later the Dock in System: System.
You can assign it just as it's made in the GAAE version:
In user-startup (ed s:user-startup) you have to add:
Assign >NIL: Dock: SYS:System/Dock/Files
But later you'll have to copy all the programs Dock has there in it's drawers:
To start, System:Programs/Games from the GAAE version.
For Shell to copy the directory Command in System
For DirOpus I've copied the one of GAAL and then copied again the lib dopus.library of Dopus libs in System libs (don't know why it wasn't working before).
For JIV I've copied it from the GAAL in System:C:
And that's all I think, the Dock works nice and I'm using kicktarts 3.0 and I've got the 1.3 theme; just like your image of the first post