Power_Broker:
Your explanation is quite confusing, but I'm going to take a shot in the dark.Let's say that that the RPi sends a single 16 bit number (or an Arduino-sized int) to the Arduino one byte at a time and with the MSB (most significant byte) first. If all you want to do is to combine both bytes into a single int, all you have to do is this:
The feeling is mutual on the explanation thing 
Cause I am not quite understanding yours either. It just seems like this should be an easy thing to do, you know? So the serial coming in is kind of a constant flow of the same number (that way readSpectrometer keeps running). So RPi sends: 100..... 100..... 100.... Until the RPi program stops and then the user pick something else: 1500.....1500....1500..... (RPi is looping).
I also tried something simple:
while (!Serial.available());
int inByte = Serial.read();
if (inByte > 3500) {
digitalWrite(led, LOW);
}
and it doesn't go through the if (inByte > ..... statement at all.
aarg:
Then you want to read this:
Serial Input Basics - updated - Introductory Tutorials - Arduino Forum
I'll keep reading and trying things out from this.