Craig,
Is the coolant flow (ie water pump) sufficient? Also, do you think there may be some heat soak from the water lines along the side (counter-current heat exchange)?
What led you away from the rear air intake? Is there negative pressure in that location on the rear deck?
Are you still running the stock exhaust headers? If so, some ceramic coated headers might help with engine cooling (helped with my Viper). 3" Metallic cats might help as well.
Just thought I'd pile on some more questions!! BTW, I DO appreciate your insights. They will be very helpful in my build.