I removed one of the serial port connectors and the motherboard connectors by breaking it off carefully as detailed in Kasar's guide. The others I removed with a heat gun. I trimmed and cleaned up the areas which were modified and I didn't see any bridges that could be causing shorts.
I'm using the stock regulator board and haven't modified everything else. The board is untrimmed. The fan spins and there's warmth from the chips. I tested with a multimeter and the board is getting the proper voltages on the power connector and as well, I tested the 5v pin on the composite video connector and that is working as well. The LED for the controller connector lights up and the disk drive is fully functional. No idea what could have happened!! I'm working on a wood table. Any advice or do I need to just get a new cube?? It's a bit discouraging messing up on the first step!