The boot.efi method worked flawlessly on my 2006 Mac Pro. I just did sudo rm to remove the old file in CoreServices and sudo cp to copy the new one. Then sudo chown root:wheel on the file and sudo chflags uchg. I just followed the instructions here:
http://www.red91.com/2009/10/23/enabling-snow-leopard-64-bit-kernel/
For the file in /i386, I just replaced it with the Finder (I repaired permission afterwards).
I didn't do anything with -bless. I just rebooted from Lion an selected the Mavericks drive with the alt-key.
It's way faster than chameleon and it looks like your Mac is just supported. The system profiler even reports the correct model (Mac Pro 1.1 with xeons instead of the C2D reported under chameleon). It's absolutely flawless and I recommend that every 2006 Mac Pro owner uses this method. Everything just works.