If you have any doubt, disable all SPI devices before starting any of them. After that, you should be able to start them in any order you want.
void setup() {
// disable wifi SPI
pinMode(SSWiFi, OUTPUT);
digitalWrite(SSWiFi, HIGH);
// disable wifi shield SD SPI
pinMode(4, OUTPUT);
digitalWrite(4, HIGH);
// disable GD GPU SPI
pinMode(8, OUTPUT);
digitalWrite(8, HIGH);
// disable GD SD SPI
pinMode(9, OUTPUT);
digitalWrite(9, HIGH);
// now start the SPI devices
GD.begin();
:
: <so on>
}