uff... I am in exactly opposite situation. I mean I quit Workbench a LONG time ago and now if I start AmiKit without DOpus I am completely lost ;)
Therefore, I am afraid, you have to customize and adjust AmiKit configuration (if you run it without DOpus) by yourself. AmiKit was designed to run DOpus from the very beggining, sorry.
IMHO I believe it is worth to learn how to work with DOpus, you can get the basic idea from Total Amiga magazines, I put the links on "Features" and "Tips&Tricks" pages of English AmiKit site.
With regards to icon-speedup-patch: it is already included in AmiKit. AfA_OS makes the loading of icons as fast as "IconBeFast" program. The routines are the same in both programs anyway.