What do you get on the 5v pin?
At this point, you’re either tracking down a short that might be in the IC or support will probably tell you that you need a new controller.
pin 1: 4.7
pin 2: 4.9
pin 3: 0.0
pin 4: 4.4
pin 5: 4.9
pin 6: 0.0
Support suggested to replace the power supply pcb 
I have a spare controller with a burnt tb6600 so I am considering finding the damaged component and replacing it with the parts of the spare controller
Can you remove that variable?
Connect straight from 24v supply to main board.
Or…
If you have a regulated 5v source, you could connect 5v to pin 2 and GND to pin 6 on that ICSP header. That’ll tell you if it’s something on that PCB.
I don’t think it’s the power supply pcb as the signal is being generated somewhere from the main board it seems. The last thing support said was: “Unfortunately, it seems your X-Controller is working as intended and we do not have additional support to help you with the laser. If you would like to purchase a new power supply interface PCB, let me know!”
If the short is there, it would trace all the way back though. The short could happen anywhere from the atmega to the exterior connector.
Hopefully the issue is on that PSU PCB…that’s a cheaper fix.
I wired the main board directly to the power source without the power source pcb but I’m still getting voltage in pin 4 (PWM signal) grounding with pin 6 
The connector to the external pwm pins is disconnected?
Yes
Well, at least you didn’t buy the PCB they’re trying to sell you.
Yeah… now I need a new main board 
You’ve been very helpful. Thank you, Neil!
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Possibly just the MCU. Didn’t you say you had another x-controller?
Maybe it’s time to build your own controller with an Arduino and discreet drivers and other components?
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Hey Neil! Hope you’re doing good. I have decided to take your advice on builing my own controller with an arduino. Can you tell me where to start please? It’s time to get that laser to work.