Updated: Nov 2
I have previously used Arduino Mega and STM32 devices to capture signal data for logging and debugging. I have been working on a Teensy-based debugger. Specifically, I am using a Teensy 4.1. This should provide a fairly fast processor along with native high-speed USB support.
Above left, I have a small PCB that can take in signals through either a PCIe x4 connector or pin headers. This small PCB has four shift registers that can each take in 8 data signals in parallel and then shift out those signals through serial to the Teensy. On the right PCB, the incoming shift register serial data is converted from 5V to 3.3V (as the Teensy does not support 5V signals). The shift registers on the left PCB are controlled by the Teensy on the right PCB; the control signals are level shifted from 3.3V to 5V before going to the shift registers. One the Teensy has the signal data, it is transmitted to the PC through high-speed USB (480 Mbps).
In the following video, I have the debugger running on my 386 DX build.
Below are links to the schematics used for these two PCBs.
If you are interested in the code I am using on the Teensy or the Winforms code, drop me a note, and I can get the code posted.