which mewtwo to powerup

I definitively would have given priority to the 96% SB first as it is most relevant.

Shadow ball is the highest DPS and more versatile. It's currently very useful against mewtwo for instance.

There's no rush for your 100% since it doesn't know SB. You can decide in the future which will be its use and select the charged move accordingly.

I would suggest you level up the SB one first to somewhere level 30 as it's very useful in M2 raid itself. Then you can save the candies and use them wisely later.

First, power up your 96% Mewtwo with SB. Then power up your next Mewtwo with SB.

Anything without SB can wait until at least after Mewtwo raids end.
As ghao said, easy answer.

I would say that I agree to power up the 96 with shadow ball.

I can think of only two reasons why you would go for the 100%.
First would be showing off. Second would be if you have trouble taking out Blisseys to take over gyms in which case give your 100% psycho cut and focus blast and turn him loose.

96% definitely, the extra 2 stats doesn't surpass SB's power.
100% shouldn't be set aside though, power them both eventually as that'll still be a top-notch attacker in either Psychic, Ice, or Fighting situations.