Hi sapele and welcome to the forum
chameleon now boots and wants to start my time machine back up disk by default.
You can change which disk/partition Chameleon tries to boot by default with the following boot option in the /Extra/com.apple.Boot.plist
<key>Default Partition</key>
<string>hd(x,y)</string>
where 'x' is the disk number, 'y' the partition number.
Then I erased the 1TB WD disk and cloned the install back to it....
If I hit return to boot the 1TB disk I am informed that chameleon can't find mach_kernel.
You see that error when Chameleon tries to boot a partition without the mach_kernel file at it's root. Double check your drive cloned successfully and make sure it has the mach_kernel file at it's root. It's also worth checking your /Extra/com.apple.Boot.plist to see if it contains the following
<key>Kernel</key>
<string>mach_kernel</string>
If I then try to boot the test OS I get a KP 9 times out of 10. If I reboot the machine and try to boot the test partition fist then it will boot 9 times out of 10 without a KP.
This is not a Chameleon issue. If you are happy you have a working /Extra folder then there is something wrong with your OS X installation.
I have erased the chameleon partition and rolled back to RC2 which worked for a while until i tried to boot RC4 from a USB stick and everything has been screwy since.
Booting from a Chameleon install on a USB stick will not change anything on your HDD's and therefore won't have been the cause of messing your system.
Overall though, don't panic. I just think you have got yourself a bit muddled as to what is doing what as the whole process is really pretty simple. I recommend finding a spare partition on one of your many HDD's and doing a fresh OS installation, then see if you can boot that from your existing Chameleon install. If you can't then re-install Chameleon and your required /Extra folder to either another HDD partition or a USB memory stick and try that. Either one or both of those method will work.
Good luck