Stock Y rod weighs about 680 grams and Callies rod with estimate hp rating up to 850 hp weights 648 grams.  And the piston I think, weights only about 419 to 432 grams. So, with that combination, I would end up to 1067 or 1080 grams. So, when stock Y piston weights 555 to 585 grams, I could save about 200 grams in every cylinder and that makes 1,6 kilos total. and there is some lighter piston pins too... 20 grams lighter atleast.

So, could this be problem at the balancing shop? Without using mallory metal of course...

I would think you would need to remove weight from the crank counterweights with lighter pistons and rods.  Ted will surely chime in, he's in the balancing business.

John is right.  As long as you are making the rotating assembly (rods, pistons, rings, brgs, etc.) lighter, then rebalancing the crankshaft is simply a matter of removing weight from the counterweights to get the crankshaft back in a state of balance that matches whatever bobweight value you end up using.  It’s when the pistons and/or rods are heavier than stock that the use of heavy metal, Mallory, or tungsten may be required.