Hello and sorry for the delay.
I answer your last question first. "Amiga Forever" package does not contain all the files compared to AmigaOS3.9 CD. However these missing files are not very important because they are not direct part of the core OS. Some of them like EditPad are replaced by microgolded alternative anyway, etc. Read more here
If you used AmigaForever as the source of the system files for AmiKit, it is enough to copy those few missing files from your AmigaOS3.9 CD manually. No need for complete re-installation.
With regards to your problem with starting up the AmiKit, I recommend to re-install it with AmigaOS3.9 CD again. Please follow these steps:
1) Install AmiKit 1.2.0 archive
2) Install AmiKit 1.3.0 cumulative update archive
3) Start AmiKit, import the system files from AmigaOS3.9 CD
4) Boot your AmiKit (note that the first boot takes MUCH longer because all the 1.2.0 -> 1.3.0 update archives have to be installed)
5) Once you get into desktop, the requester asks you to turn off AmiKit and start it again (this is necessary to enable DualPNG icon support)
6) Start AmiKit, once you get into desktop again, the Live Update informs you that the new on-line updates are available. Download them all and reboot your AmiKit
7) Install BoingBag 1&2 for OS3.9
8) Run "Install Patches" script located on desktop (optional)
9) ...and that's it, finally.
This procedure gets much easier as soon as the full 1.4.0 archive is released. You just install it, import OS, install both BoingBags and that's it. The update archive from 1.3.x to 1.4.0 will also be available so you don't need to re-install again, of course.