Evocati

I thought of something that I forgot to mention.
The standard PMODs are good for low toggling rate interfaces. Also they have 200 ohm series resistors that, to some extent, help protect from ESD and shorts, both temporary and long term, and to a lesser extent transmission line issues. Even still try and keep cabling as short as possible, especially with flying leads.

I've done this many times. What boards are your using?
Tips:
make sure that you have a good bonding of the GND reference for both boards, especially for single-ended signals. PMODs have 2 GND pins. Don't connect any power rail of both boards together Before configuring both boards as a connected system take extra precautions to be sure that your have assigned the pin locations correctly; that is check the post route pin assignments. Make sure that there is no possibility of contention. The pin on the sink side should be an input only and the pin on the source side should be an output only. For relatively slow signalling assign output driver SLEW as slow and output drive at 4 mA or the minimum available for the first test. Open-drain or open collector outputs are one way to connect drivers safely. The safest way to connect external hardware is through external buffers as a protection for the FPGA pins. Before powering anything double or triple check the interface wiring and design. Be aware that the PMODs are not keyed... so it is possible to have connection/cabling issues with potentially disastrous consequences.   You don't want to tie the GND and VCC together or drive output buffers into either of those rails. What exactly are your concerns?