I've got it working. The problem is that all the patches are installed from the ISO but some of the names are cut off. If you look in the subdirectory 'pkgs' you'll find these files:
kernel-2.6.29.6-fix-a-bug-of-Intel-PRO-1000-PCI-Ex
kernel-2.6.29.6-fix-a-bug-of-Intel-PRO-1000-PCI-Ex
If you rename these to the files that are missing:
kernel-2.6.29.6-fix-a-bug-of-Intel-PRO-1000-PCI-Express-Gigabit-Ethernet-driver.patch
kernel-2.6.29.6-fix-a-bug-of-Intel-PRO-1000-PCI-Express-Gigabit-Ethernet-driver.patch.md5
then the error disappears. I had to rename one other file:
kernel-2.6.29.6-mpc8308wmg-mpc8308rdb-mpc8308seg-d
to:
kernel-2.6.29.6-mpc8308wmg-mpc8308rdb-mpc8308seg-d
My build has just completed!