It sounds like you did everything correctly. Wound the clock when first touched by R, bagged the recovery of a kick inside the 5 and correctly let the play continue.
Your understanding of the rule is correct. A kick that breaks the plane of R's goal line is dead. As soon as the ball was possessed in the field of play, it was no longer a kick. There is nothing preventing Team R from running a live ball out of the end zone.
Good job!
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Even if you’re on the right track, you’ll get run over if you just sit there. - Will Rogers
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