JTAG to send a syncronized pulse to a large chained set of dev kits?

Does your PCI express motherboard support JTAG, do you have software drivers to operate it?

In principle (by design of the JTAG protocol), it's possible to update data registers of multiple devices in a JTAG chain simultaneously. Practically, I doubt that it's supported by standard tools, e.g. Altera Quartus.

With reasonable effort, connecting a hardware wire between the boards that propagate the trigger seems preferable. What's an acceptable delay and skew for the trigger?