Can I mod the scanner (I plan to use option 2, kraftwerk mode) to use 9 separate 5mm color LEDs (waterclear)? Will there be enough voltage? I’m assuming I’d have to use a respective resistor for each different color of LED
Yes, that should be fine if you use different resistors. You *will* need to use more voltage. 5 V is max, and you’ll need to pick the resistors according to the voltage that you use. I’d recommend 4.5 V, as in 3 x AA cells.