@epicurean . I put something together for you, please PM me an email address and I'll email you the file.
I made a simple flat plate. Because I don't have the exact case and motherboard in front of me, or exact measurements of the I/O Shield, like detailed measurements of the "lip" that the metal shields have to snap into place and etc. trying to replicate that just wouldn't work.
I started with a 1U backplate I found online at Thingiverse.com for the A1SAI/A1SRI motherboards. These boards use the same exact I/O shield part number as your board. They just make use of different hole knockouts.
1U IO Shield/Backplate for Supermicro A1SAI/A1SRI Mainboards by 3DMK
The overall size of this plate didn't match the measurements of yours though, and the height of the component openings was different. So I adjusted for that. In one of your photos of the I/O shield that came with the case, it appeared that the vertical center of the lowest USB opening was ~10mm, so I adjusted the height of the component openings based on that.
Lastly, the model at the link above was quite thick, 1.5mm. I made this one 0.5mm, so to be closer to the thickness of the metal version. I understand PET-G can go down to 0.2mm but at that thickness, successful prints are difficult.
As for learning, the program
@RimBlock recommends looks to have more features than TInkercad, but not so many that it will be overwhelming. My preference for Tinkercad is mostly due to it being online. I do educational training for kids at their school classrooms for multiple schools in the region. Not having to have kids/teachers load a program on classroom computers when we visit is a big plus. But, since you have your own computer, installing an application isn't an issue.
To get up and running on 3D prints for your projects, you may want to spend a bit of time browsing/searching file library sites like thingiverse.com. For lot of projects, like this I/O shield, you will often find a file you can modify for use, or if you are lucky, one already designed for your specific purpose. Many sites, again like Thingiverse, make the files freely available. There's a provision to provide a payment of your choice to the creator if you wish, but its optional. Starting with a file that's close to what you need can save you some time.