1. The last legal down was a legal kick play
2. The game clock is stopped to award team R a new series
3. The play clock is set to 25 seconds by rule in 3-6-1-a-1-f
4. And starts on the RFP
Fully agree. No argument here. After the kick play, play clock is set to :25.
After an officials timeout due to a defensive injury, equipment issue or penalty, the above becomes irrelevant and now we look at 3-6-1-a-1-e Exceptions and reset the play clock to :40 to restart the play.
Our guidance based on what I believe is the clear wording in the rule is we complete the penalty, reset the play clock back to the original 25 and move on. We have been clearly instructed that if we had a 25 second play clock that was interrupted by a flag or any other official timeout then that is where we reset the play clock to.
If that's the guidance you've been given, then do that, but there's no rule justification for it.