You didn't mention which version of AF you were trying (I'm going to assume AF 2008, since there are "issues" with AF2008 & AmiKit).
Among other things, there was a change in the ROMs that made it impossible for the ROMFind utility to recognize them.
The next version of AmiKit fixes all these issues. I'm hopeful that it's release is IMMINENT.
In the interim, try this (if you haven't already) ...
Install AF first -- make sure that it is set up and working correctly.
Replace the version of WinUAE included with AmiKit with the latest one from http://www.winuae.net/.
When AmiKit asks for a source of system files, there's supposed to be an option for using an installed version of AF (never done this -- going from memory).
If this doesn't help, rest assured that AmiKit 1.5 fixes the problems with AF 2008 and should be released soon (like YESTERDAY if I have my way!