Assuming the FIDE rules allow you to record on the Monroi before moving (in this case) I would have no problem using that rule in a FIDE tournament. In a USCF tournament, using the current rules I would require the 14C4 method for a Monroi user to claim three-fold repetition (move, determining the move, and then claim prior to hitting the clock and completing the move).
First of all, Black’s claim was short by a full move (2 plies), not just half a move (1 ply), so you were correct to deny (for the time being) Black’s claim.
A far more interesting question (for discussion purposes) is, how should the TD rule if Black had made his 98th move, and then White (rather than Black) had claimed a draw. This claim would be only half a move (1 ply) short, and White would be in a position to play the missing half-move, thus generating the full 50-move situation.
The 50-move rule ought to be parallel to the triple occurrence rule in this regard. With a triple occurrence, a player who is in a position to create the third occurrence is allowed to claim (even though he is momentarily a half-move short) based on an intended move. Then, if his claim turns out to be incorrect, he is still obligated to play the intended move.
The 50-move rule should work the same way. If there have been only 49.5 moves (99 plies), a player who is in a position to play the 100th ply should be allowed to claim based on his intended move.
Unfortunately, the rule doesn’t currently say this, so a TD is forced into other alternatives, such as asking the player to first play the move, then neutralize (rather than press) the clock, then await the ruling.
Bill Smythe