I've managed to update my system.
Here's what I did:

Extracted MacOSXUpdCombo10.5.4.pkg (using Pacifist)
Patched and decrypted all files
Deleted these files (from the extracted files):
- mach_kernel
- mach_kernel.ctfsys
- System.kext
- IONetworkingFamily.kext (if you use a patched one)
- AppleSMBios.kext
- AppleEFIRuntime.kext
- AppleIntelCPUPowerManagement
- AppleACPIPlatform.kext (if you don't use EFI)
- NVidia kexts

Rebuilt the package (using Packagemaker 2.1).
Installed patched update
Installed StageXNU kernel and System.kext
Cleaned Kext caches.
Rebooted with "-v -f" flags.

and...
Voila! xD