Verilog works in simulation but not FPGA hardware
It appears that you connected the 5V I/O of the Arduino Uno directly to the 3.3V I/O of the FPGA. That's probably the primary source of your problems.

Here's hoping that you haven't actually damaged the FPGA with the overvoltage. At least the current is somewhat limited by the microcontroller.


  Are ringing and crosstalk related to the current/slew settings in the pin planner in Quartus?


No, that would only apply to outputs from the FPGA. The signals from the Arduino are inputs.