This is all very manual, but I have 100% success rate (without damaging the cable or the motherboard) with my caveman approach.

I leave the pins as is on the motherboard. For the breakout cable, I would apply firm (but not gorilla) force and the pin pushes through the block off. I usually run into this with newer floppy and/or IDE ribbon cables connecting to older boards.

If you have reason to believe the block off is a solid lump of plastic (usually it's white, but I don't recall if I have seen this on any USB cable I've had to work with; it's been just been a thin layer of the same black plastic with which the connector was made), you could modify (if necessary) the cable to allow it to eject out the back end while it is pushed from the front end. I'm not sure if you have to modify the cable boot (if there is one) in your case.

It's personally preference. I've modified USB cables with a hot needle to add the hole, but I've also broke the pin off of a non-keyed IDE motherboard header so I could use the common keyed cables. You can also just bend the pin off to the side.

I use these style of USB plates on AT motherboards and adjust them as necessary:

There simply are two different styles of USB header around.

The missing leg:

And the Zig-Zag:

The former has a missing pin and hole to code its polarity while the latter is rotation symmetrical, not caring about its orientation.

It is generally advisable to attach the USB bracket the right way. The single or two black cables is ground.
The two plug type of bracket, as shown earlier, allows for both.
If need be, the generic Dupont plugs can be replaced or the pins in it rearranged.

Repo Man11 wrote on 2022-04-18, 20:42:

I use these style of USB plates on AT motherboards and adjust them as necessary:

Thanks! That looks like what the board expects me to use, where each port has a separate 5 pin connector.

Cuttoon wrote on 2022-04-18, 21:07:

There simply are two different styles of USB header around. […]
Show full quote

There simply are two different styles of USB header around.

The missing leg:

The attachment usb1.gif is no longer available

And the Zig-Zag:

The attachment usb2.jpeg is no longer available

The former has a missing pin and hole to code its polarity while the latter is rotation symmetrical, not caring about its orientation.

It is generally advisable to attach the USB bracket the right way. The single or two black cables is ground.
The two plug type of bracket, as shown earlier, allows for both.
If need be, the generic Dupont plugs can be replaced or the pins in it rearranged.

Ahhh that makes sense, I didn't know about the zig-zag style of header. Mine is the missing leg version (updated original post with pinout) so the connector I have should work if I can get around the extra pin issue.

Thanks all for the help and knowledge! :)

Meatball wrote on 2022-04-18, 19:52:

I leave the pins as is on the motherboard. For the breakout cable, I would apply firm (but not gorilla) force and the pin pushes through the block off. I usually run into this with newer floppy and/or IDE ribbon cables connecting to older boards.

This worked! I didn't think to try pushing the plastic out from the cable side of the connector. I used a small sharp pin and made a hole where pin 9 should be on the connector and plugged it in. Just copied some files over USB for the first time on this board. 8)

Thanks everyone!

Looking in the manual, the connector is like the first image Cuttoon shared, except that instead of a Key at pin 9, it has another NC pin, so it would be possible to cut it off without ever affecting use.