Is Rock-Paper-Scissors played by pumping my arm 2 times then throwing my choice, or pumping 3 times then throw?
According to the current "Play! Pokemon TCG Tournament Rules and Formats" document, the procedure is a three-count priming and then the simultaneous throw of the choice, for example, "Rock-Paper-Scissors-Shoot" with the choice thrown on "shoot".
Source: PUI Rules Team (2008-10-16), TPCi Rules Team (2013-11-21)
Can I use dice or cards to indicate my throw in Rock-Paper-Scissors?
You may not use dice to indicate your choice, as it is too easy to manipulate the dice while it is covered. The requirements for R-P-S cards are that they must have identical backs, that they clearly say "Rock" or "Paper" or "Scissors" on the front and that all themes on the cards be appropriate for a Pokemon Event as determined by the Head Judge.
Source: PUI Rules Team (2008-10-16)
Is it OK to roll a dice to randomize my Rock-Paper-Scissors choice?
No. R-P-S is a game of strategy. You must not appear to be randomizing your choice by any method.
Source: PUI Rules Team (2008-10-16)