Where was Shinji Matou during Fate/Zero?

Question

In Fate/Zero, we see that the Matou don't really have a proper candidate to participate in the war. So Zouken adopted Sakura. Then Kariya comes up and participates. In exchange for winning the grail, Zouken will release Sakura from her fate as a mage (?).

Then Kariya loses. Therefore Zouken still needs Sakura, does he not? Zouken will continue training her to participate in the next war.

But, in Fate Stay/Night and UBW, this is the situation:

• Sakura is a normal girl with no apparent knowledge of magic.
• Shinji Matou is the master fighting for the Matou family.

Then, my question is:

• Where was Shinji Matou during Fate/Zero? Why did Zouken need Sakura if he had Shinji?

Answer 1

Where was Shinji Matou during Fate/Zero?

Shinji was overseas at the time. He is only mentioned by his father Byakuya in the original Novel.

He was briefly mentioned by Byakuya in the original Fate/Zero novel, his only child was sent overseas in the name of studying.

Source: Shinji Matou - Other Appearances

Why did Zouken need Sakura if he had Shinji?

The original reason Zouken adopted Sakura was because Shinji was inferior as a magus due to their declining bloodline and wasn't fit to be an heir. Shinji stated in the Fate Route that this was because the Matou didn't properly adopt to the land, as they were foreigners to Japan, unlike the Tohsaka.

Furthermore, since having two heirs would weaken the inheritance (magic) that is to be passed down, and raising both as magi is always believed to cause conflict between the siblings down the track (as was the case with the Aozaki family), the Tohsaka's, like any other magus family, can only choose one heir.

Because the Tohsaka's and Matou's were ancient allies back from when the 3 families were tutored by Kischur Zelretch Schweinorg, Tokiomi Tohsaka put Sakura up for adoption to the Matou.

Like most magi, her father chose only one daughter to carry on his family's tradition as he believed raising an additional child would introduce competition. Zouken Matou, an ancient ally of the Tohsaka House, offered to adopt Sakura with the intention of training her as the successor of the Matou's magecraft as his own heir, Shinji, was incapable of sorcery.

Source: Sakura Matou - Background

The reason why Rin was chosen over Sakura was because Rin's Elemental Affinity was all five, while Sakura's was Imaginary Numbers. However, it was during her "training" which forcefully changed her Elemental Affinity to Water (Matou standard) that Zouken saw her potential as a Master.

As for Shinji Matou being a Master, he was a fake Master. From the beginning, Sakura was the Matou's Master. The book Shinji is shown to hold when he commanded Rider was the Book of the False Attendant, which was created from one of Sakura's Command Spells. Because the book cut Rider's Prana supply from Sakura but didn't change the source to Shinji, Rider needed other ways to gain Parana to stay manifested, thus the set up for Blood Fort Andromeda. Sakura made the book for Shinji to use, as she did not want to fight in the War because

1. She could hurt Shirou (at that time, she was not aware that he had become a Master)
2. She would hurt Rin (despite being told by Zouken to think of her former family as dead, she still recognized Rin as her sister)

Sakura was only forced to fight in the war in the Heaven's Feel Route when Shinji splashed something on Sakura during the Blood Fort's activation, causing the worms inside Sakura to go crazy. This forced her to fight in the war and put an end to it, lest she be consumed by the worms.

Answer 2

Where was Shinji Matou during Fate/Zero?

Well, he was five years old at the time. I guess that during Fate/Zero, he was hanging around the Matou residence or something.

Why did Zouken need Sakura if he had Shinji?

Heaven's Feel spoilers (I think?):

Shinji is a non-mage, like his father (Byakuya), and thus essentially useless to Zouken. This, again, was the whole point behind having Sakura adopted in from the Tohsaka family - Kariya was unwilling to cooperate, and Byakuya was a non-mage (and so would all his offspring be).

But, you say, Shinji is a Master in the fifth war! How can that be? Well, it turns out that Rider's actual master is Sakura. Basically, Shinji torments Sakura until she surrenders provisional control of Rider to Shinji by means of a magical book that behaves like a Command Spell.

So anyway, Shinji, like Kariya, did not really factor into Zouken's plans. With both of them, it would have been nice if they won the war, but Zouken's ultimate plans revolved around Sakura. During Fate/Zero, his plan was for Sakura's offspring to win the fifth war; but when the fifth war came around fifty-ish years early, his goal was to have Sakura herself win the war on his behalf. This obviously doesn't work out well for Zouken in Fate or UBW, but he comes pretty close to getting what he wants in Heaven's Feel.

This whole confusion you're having is one of the big reasons why watching Fate/Zero before Heaven's Feel makes for a somewhat subpar experience - knowing in advance that Zouken has all these sinister plans, you can't help but wonder what he's been up to in the first two routes and what the whole deal with Sakura and Shinji is and so forth.