I've run the GN-1 valve covers in the past myself. Basically you have two choices.
1. Clearance the heck out of the heat shied, IE: taking a nice sized hammer to the heat shield. Motor out of the car of course.
2. Remove the heat shield completely and no other modifications will be required. However, the motor will need to be out of the way in order to get to the two 9/32 head screws that bolt the heatshield to the heater box/firewall. You might be able to pulls the motor mount on the drivers side and slowly let the motor down using a picker, it should rotate over to gain a little clearance with removing the shield, but don't know, never tried that. The downpipe would have to be disconnected for sure tho.
I chose #2 and never had any problems getting the valve cover on or off with the motor in the car. No heat related issues either.
HTH
Patrick