Yeah, when I had a MDD in hand and contempalted what could be done I considerd using PCI riser cards, too. Or are you extending the video connectors of the built-in graphics to the back?
How exactly did you adapt those USB3 connectors to the plate of the PCI slot? When I was working on my mods I considered such a solution too. Reason I didn't do it is that I didn't see a way to cleanly cut the metal plates. So I went with 3D printed parts to bring out the USB and audio ports through the ZIP drive slot in the front. Are you using parts that can be ordered online or did you cut it yourself?
What motherboard are you using?
The USB bracket is a standard USB 3 extension slot for internal headers with a extension, you can find them everywhere on Ebay or Amazon.
The graficports are extended from the motherboard with extensions i found on Aliexpress and a empty slot bracket for DVI and HDMI, also Aliexpress.
The MB is a Asus B150 wifi/aura with an i5, a leftover from my G4 Cube Mod.