According to him, the stone/metal replacement bodyparts have no mass or density and do not contribute to his composite body weight.
I'm all for interesting. I'm not for 'crap you couldn't do sober, healthy, and with twenty years to make it work'. I'm good with letting him have spirit/magic-infused replacements for his limbs; insert my evil GM smile, because doing
that is going to get magic-research people Very Interested Indeed. But you should inform him if they have no mass or density, contributing nothing to his weight, he's going to have to make an Agility (2) test to take a step. And again to take another one. And again ... you get the idea. He may mean no
additional mass/density beyond what his ordinary fleshy limbs were, but I'd still give him the option to either have them at the 30kg weight of a stone leg and the 15kg weight of a stone arm, or else be running with a constant dice pool penalty for sustaining a spell -- levitate, or something similar.
Cool stuff is cool. It also has built-in disadvantages.
My questions:
1. Should I have taken an Essence Deduction as he is not a "whole" person?
2. Should I take into account his stone/metal appendages when completing stealth, body, and agility test?
See others' commentaries above. My replies are 1) yes, and 2) yes. If not, well ...
GM tip: give the players one (1) chance to convince you. Inform them of this fact at campaign start, and that if they don't make an absolutely compelling argument, then your adjudication stands. You may, if you are feeling kind, inform him of the consequences of his desires. "Magic limbs with no weight and no essence loss!!" equals 'GM is sending snatch teams after my character twice every session, and once in-between runs." By Run #5, they'll be kill teams with orders to just bring back the limbs. If by some miracle he remains alive and free by Run #10, pull out all the stops -- kill / blackmail all of his contacts, all of his friends, blow up his favorite bar, send a mage-defended attack helo after him on the I-5 bridge to blow his ass into puree. Have corporate mage-research VPs make calls to his teammates, offering direct bounties on his head -- or at least his limbs. If they don't play ball, then kill his teammate's contacts.
Cool stuff is cool. A player should always be aware, though, that other people want the Cool, and
every GM should make that a major point. When a GM says 'Okay!' to a player saying 'I'm neat!', the player should get nervous.