you can just replace the boot.img in the zip file
I dont know how to write update.zip's sorry i will look into this
Use the 'anykernel' method. It's way easier.
- get Anykernel:
git clone https://github.com/koush/AnyKernel - Delete any modules that came with AnyKernel
rm <AnyKernelPath>/system/lib/modules/* - replace zImage in the kernel/ folder
cp <kernel path>/arch/arm/mach-msm/zImage <AnyKernelPath>/kernel - Copy modules over (generally, just wifi)
cp <module path and ifle name> <AnyKernelPath>/system/lib/modules - Create flashable zip:
cd <AnyKernelPath>
zip -r newkernel.zip *