I didn't read the whole thread, but if the motherboard had USB headers and you wired them wrong (early USB headers weren't standard) and plugged something in, you could have shorted the 5v rail to ground and damaged something.
I did not. When I discovered the USB header was non-standard, I abandoned the onboard USB and focused my efforts on USB peripheral cards.
Here's what happened:
I first installed a SIIG JU-P20012 USB 1.1 card I have new-old-stock that works in other PCs. It did not work in this machine, '95 couldn't find the drivers. I found this download pack on archive.org:
https://archive.org/details/drivers-usb-1.1-2.0-for-win-95-mac but my SIIG card has a sticker over the chip I am unwilling to peel off.
Next I tried a USB 2.0 card from my bin with an NEC chip and the NEC drivers from the IA pack. But I couldn't figure out how to point '95 at the correct driver file and it couldn't find the drivers when I put them on a virtual floppy.
I then decided to try a new-old-stock card with an NEC chip that I have an actual driver CD for. This is when the issue started. First it got into windows, started detecting the card, and then the screen went black. Then it stopped posting. I took the card out, it posted a few times with an I/O error, now it won't post at all.
I don't THINK the problem was the USB card itself. I followed standard troubleshooting and took out the new card, then the other new card, then every card except the graphics card. No joy. My beautiful little AT machine will not post.