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Serial1 on the Arduino Leonardo is hardware serial, not software.

There are several ways to read in multiple bytes from Serial.

Instead of detecting Serial.available() (i.e. non-zero), change it to Serial.available() >= 2

if (Serial.available() >= 2) {
 for (int i=0; i<2; i++) {
 buffer[i] = Serial.read();
 }
}

Or you can leave it as it is, and read into the buffer one at a time.

static int bufferIndex;
if (Serial.available())
{
 buffer[bufferIndex++] = Serial.read()
}

You'll need to detect the contents of the buffer in another if statement, and also deal with the bounds of the index.

Honestly though, noise is your issue here - this is an example of an XY problem. There's nothing inherent in using a microcontroller with relays that should mean that serial won't work.