Did you fastboot flash the MCR's boot image?
Thanks for working on this. The permissions look ok on the file, I dont have the phone to hand, but from memory, it has execute permissions. As an FYI, I tried another init.d script and that didn't execute on boot either.
I need to make it more explicit in instructions and when applying the update zip that that is necessary if S-ON. I'm S-OFF so I forget! :-)