I'm interested in what exercises/training I can do to help with reaction time and timing for martial arts. Specifically, how can I improve parrying and countering a strike? I'm not looking for speed drills (speed is different than reaction time and timing). I need to be able to react based on some cue and then determine the on-coming strike speed so I can appropriately parry it and counter...any suggestions?
Anderson Silva, who is what one could conservatively call one of the most successful counter-punchers in modern mixed martial arts, includes two elements in his training that I would say are vital to that success:
Other than footwork drills for agility, conditioning work to make sure you're fresh enough to present an intelligent defense, drilling boxing defense and head movement techniques, and power training to develop explosiveness, I would focus on these two methods (mostly the first) for improving one's martial arts reaction time.
Given that you seem to be very experienced in the field, i.e. know all the technical aspects of the situations back and forth, and assuming that you are fit, it might make sense to focus on meditation.
Over time, meditation can help you with of seeing the situation as it really is and that might be better for reaction speed and timing than basing the reaction pattern on a specific cue.
My own experience from playing basketball is that I was more likely to get into a "flow" state (i.e. where your opponents seems to be in slow motion) if I have had the possibility to meditate before the games.
Besides meditating before home games, I did it 15-20 minutes twice a day, just based on reading about it, not following any particular meditation school.