There's a program that will sort roll-ups for you
http://forum.xda-developers.com/showthread.php?t=542081
If your SYS rollup is properly sorted, for example
4090
COMMON
LangDB
MSXIPKernel
MSXIPKernelTKL
You'll want to move the folders from 4090 into the COMMON folder.
Open the PreKitchen Tool and browse for the COMMON folder.
Under Sorting, Tick "Into SYS layout for the Ervius Kitchen"
Then hit Go.
Your COMMON folder contents should now look like this:
dpi_96
dpi_96_resh_240_resv_230
dpi_96_resh_240_resv_400
dpi_192
dpi_192_resh_480_resv_640
dpi_192_resh_480_resv_800
SHARED
Remove the unnecessary DPI resolution folders if needed.
(dpi_96*)
Rename the COMMON folder to what ever sys version you dumped (23659) and drop it into your kitchen's SYS folder.
The remaining folders (LangDB, MSXIPKernel, MSXIPKernelLTK) would belong to
x:\kitchen\ROM\Shared\23659
Don't forget to copy and rename an OEMXipKernel to match this sys version
x:\kitchen\ROM\Diamond\