I figured this out after the first assembly but it's easier if you remove the Y 4040 extrusion off the frame and install the motherboard enclosure into the frame.

It is a very tight fit especially with the bed still on the printer.

6x M3x8 countersunk screws and 6x T-nuts secure it to the inside of the frame.

Secure the motherboard enclosure into the frame with 4x M5x10 button head screws on the front where you tapped the threads

2x M3x8 socket head screws and 2x T nuts secure it to the underside of the Y 4040