Hi Joel,
I can't do a whole lot blind but you are welcome to send me a board :-).
But these pins are the physical connections so if you change the pin in code, you have to actually reroute them using jumper wires. For now, pull the shield off the Lightuino and use jumper wires. Connect GND and 5v. Next connect analog 0 and 1. Finally (this is the difference) connect Lightuino 0,1 to pins 4,5 on the shield. ASIDE: Honestly I would use analog 2,3 (yes you can use the analog input pins as digital outputs -- search for it in the Arduino forums) -- but only because its nice to leave the UART (Serial.begin()) alone in case you need it later.
This is the code I got from website (see below). You'd now go through this and change every reference to pin 4 to 0 and pin 5 to 1. At that point it should work! Get your whole sketch working at this point to make sure you don't run out of CPU speed or memory.
When ready, you can think about how to do it permanently (i.e. with the shield plugged in). If you look just above the digital pins on the Lightuino, you will see a bunch of tiny holes. These are the same digital pins in the header, so you could solder jumpers there. Then its often possible to gently bend the pins on the shield that you don't want to go straight thru (in this case pins 4,5). Or worst case you can clip them or bend 'em 90 degrees so they stick straight out. Now bring your jumper wires around the top and plug them into the header at 4,5 on the shield (or solder them to the bent pins).
// Spectrum analyzer read values will be kept here.
int SpectrumLeft[7];
int SpectrumRight[7];
//Setup pins to drive the spectrum analyzer. It needs RESET and STROBE pins.
pinMode(5, OUTPUT);
pinMode(4, OUTPUT);
//Init spectrum analyzer
digitalWrite(4,LOW); //pin 4 is strobe on shield
digitalWrite(5,HIGH); //pin 5 is RESET on the shield
digitalWrite(4,HIGH);
digitalWrite(4,LOW);
digitalWrite(5,LOW);
// Function to read 7 band equalizers
void readSpectrum()
{
// Band 0 = Lowest Frequencies.
byte Band;
for(Band=0;Band <7; Band++)
{
SpectrumLeft[Band] = analogRead(0); //left
SpectrumRight[Band] = analogRead(1) //right
digitalWrite(4,HIGH); //Strobe pin on the shield
digitalWrite(4,LOW);