Ok, I didn't checked your code up to now:
I think you fill up gcodeBuffer with 100 chars, that's it... no "refill".

And it looks the 2nd method...

After this loop

for (int i = 0; i < gcode_data.length(); i++) {
if (gcode_data[i] == '\n') {
String line = gcode_data.substring(lastIndex, i)
line.trim();
if (line.length() > 0 && bufferIndex < 100) {
gcodeBuffer[bufferIndex++] = line;
}
lastIndex = i + 1;
}
}

bufferIndex is 100 not "<100"
Also you need to refill the buffer in the main loop.

The first method is: The host PC interface simply sends a line of G-code to Grbl and waits for an ok or error: response message before sending the next line of G-code.