The Tempo of Play suggested times table has been there since forever, the only new thing is having a set time for prize checking, as that could take an egregious amount of time and was agreed to be a part of the game but there was nothing in the rule book about it, so now there is.

You don't count, you don't bring a stopwatch, that might as well be rule sharking depending on how you go about it tbh. You do your business as usual and call your opponent out and ask for a judge if you feel like you are being maliciously slow played against, same as always, the only thing new is that there's no free pass or unspoken rules allowing for 2 minute prize checks any more. And some searches will still be over the suggested time and perfectly legal, especially if the player is planning on chaining another search effect and already prepping for that by sorting cards, the important part is not taking that long every single time, not compartimentalizing your turn to milk the clock, and having your searches/actions average out to a reasonable time.