The MY99 pistons with the square relief ARE taller than the MY00 pistons with the cut valve reliefs. We noticed this on 8Complex's car when he had the engine apart. The older pistons came slightly above the level of his deck, so he couldn't use them in his MY00.
Your pistons may possibly be designed for the DOHC head as well....
Your pistons may possibly be designed for the DOHC head as well....