You could download a cad version of an i/o shield and change it to fit your needs and have it printed. You're skills help you.

Sadly I do not have access to a 3D printer  I'd have to outsource the printing, and it doesn't bother me enough to put in the effort. I had honestly forgotten about it til I took these photos. (As in me posting these photos was the first time I notice, since when I plug in the ports, I'm above the case looking down so my perspective doesn't highlight the fact that it's missing). 

True. I'm weird though. I like having an i/o shield, makes it feel clean.

I really wish that there were more mini itx cases with handles on them.