[ After some time ]
Shirou was exhausted and breathing heavily. He knew that others could have done more. He again realized if he wanted to surpass the monsters in this world, Shirou wouldn't be enough. He was already aware that while the original Shirou had powerful strength and abilities, he was also very weak. You see Shirou Emiya had low magic reserves. This limited the usage of his powers. He had to focus more on technique and tactics. Even counter-guardian Shirou Emiya would lose to stronger servants like Lancer in a fair fight. Shirou Emiya's greatest strength was his will. He managed to survive the Fuyuki fire, he fought through pain comparable to inserting a hot iron rod into his spine when he inadvertently and temporarily converted his nerves into magic circuits, he even fought using Archer's arm despite knowing it was destroying his mind, body and soul, the list goes on.
If Shirou was put in the original Shirou's place, he could never imagine doing any of the things the original Shirou did in any of the timelines. That's why Shirou knows he can't depend on his current potential. He knew his will was weaker. The threats in this world are not something he can handle even at his full potential. He needs to break his limit. He needs to upgrade his mind, body and soul. Not just for his survival, but for his freedom and to have cool overpowered abilities.
Shirou believes that the key to breaking his limits lies in the basic spells he is trying to recreate. Once he manages to achieve mastery beyond a certain level, beyond any of the original Shirous levels, he will be able to transcend his limits.
[ After a few months ]
Shirou continued training his spells and doing exercises. Structural Analysis was his main focus. When he had managed to grasp the limit of an object's existence, he started recreating the reinforcement spell. He was able to figure it out and managed to practice it to an acceptable level. But it took a lot of time. This is because Shirou's Reinforcement spell has 2 steps, unlike Structural Analysis which has only 1. First Shirou uses Structural Analysis to understand the object's structure and its existential limit. Then he passes magic power through the structure without exceeding the limit. He had to break a lot of objects to make progress. To achieve perfection, even more objects need to be sacrificed. But he needs to be able to do this as only then could he reinforce his body to the max without killing himself.
Shirou also recreated Alteration and Projection. Which were also spells with 2 steps. He found some blunt beat-up ninja swords in one of the rooms in the orphanage. He started using them for spell practice. Swords will be the first objects to undergo spell practice as they are the easiest to get results from. Then Shirou would repeat the same for non-sword objects. With the previous experience, he knows how and what to look for. He just needs to train his magic and focus until he gets the same results.
He had tried to recreate Tracing as well but it is still not complete. This is due to tracing consisting of more than 2 steps. His state of mind is not yet capable of handling spells with more than 2 steps. The reason he didn't take much more time to learn 2 step spells is due to his high spiritual energy.
Shirou had begun increasing his strength. He ran until he reached his limits every day. He did other exercises as well. Once it started becoming easy, he would increase the intensity. He was exhausted by the end of each day. The progress in strength is really slow.
He had spent some time each day in the Library searching for any valuable information regarding chakra, biology, weaponsmithing, sealing techniques, anything he found useful. Fuinjutsu and weaponsmithing were his main focus in the library. Shirou was also checking the feasibility of some ideas in animes and fan fiction. He found that some are not possible to be realized but others can be implemented.
Shirou had succeeded in sensing his soul and magic circuits, it was easier than he imagined. With a few tries, he was able to trace the path along his Tenketsu to his brain and finally managed to sense his soul and magic circuits. Shirou initially thought that his soul would be something like a translucent blue sphere but he was totally wrong. He could only sense a small part of it. Even that part was too complex to comprehend. The picture in his mind could only be described as an incredibly complex ethereal energy system. Blue energy waves pulse through unknown astral structures. The moment he sensed this he felt an incredible pulling force. He was a passenger going along the ride now. It was like he suddenly started flying, no he was falling forward without end. When it finally ended he knew he arrived at the epicenter of all this. There he sensed it, 27 circuit-like lines waiting for activation, waiting for his magic energy to pass through.
'Wait for me.' - Shirou had thought at the time.
Shirou also decided he should learn how the entire system works. It could show a way to break his limits. Even though he knew the chances were really low, he wanted to see if with time he could somehow recreate Third Magic.
When Shirou stopped his magic he began falling from the Astral realm as he felt a familiar pulling force and woke up back in the real world.
'That was so trippy.' - Shirou had thought at the time.
Shirou had figured out a way to test the "natural energy petrification effect via magic circuits" problem. He would catch a fish or mice or something. Using his magic power he would try to turn one of the nerves in the specimen into a makeshift magic circuit and see if activating it will cause petrification by absorbing natural energy. He really hopes there won't be petrification and mana will be absorbed. He does not want to think about the worst-case results.
Progress in Fuinjutsu is not too bad. He still hasn't deciphered the inner workings. He can copy the seals and make some minor modifications. But creating a seal of his own is still not yet possible. It's like trying to learn a programming language without learning the high-end theories. You are only taught the basics. Shirou knew why, it is the same reason why advanced Jutsus, forbidden Jutsus and clan techniques are all kept secret. This does not mean it's impossible, as long as Shirou gathers more knowledge and experiments more with seals. He will one day be able to create his own seals. He could even create his own sealing language.
As time went on, Shirou sort of became a machine. Following a daily routine. The other children at the orphanage did not notice it as strange as Shirou was always kind of a loner. He rarely talks to others except a few like Akira and Ishida.
Ishida knew what Shirou was like. He always checked on him to make sure Shirou did not overdo anything. Ishida was also looking into Shirou's job request. Akira on the other hand confronted Shirou about why he stopped talking to everyone. Shirou was so busy with all of his training that he had forgotten that he completely stopped talking with Akira. Feeling a bit guilty Shirou explained the situation to Akira. His body condition and training plans to get stronger. Of course, he did not reveal everything. Akira did not expect Shirou wold have such a condition, so he decided to help Shirou in his training when he could. Sometimes both of them could be seen running around the village together in joint training.
Shirou even passed by Might Guy and his father Might Duy who were also doing their training. As they passed by the father and son duo gave a big smile to Shirou, in return, Shirou smiled back in kind.
"See that son, so young and working so hard. Let us run a 100 laps more." - Duy.
"YEAH.." - Guy.
Overhearing their screams, Shirou couldn't help but cringe a little, but he also felt a deep respect for them. To ignore all the comments about how they will never become great ninjas and instead turn all that hate into motivation to work harder and grow stronger. That needed a special kind of strength that most people even Shirou lacked. Shirou feels that they are the true protagonists.
'In this world where bloodline and talent rule supreme, you two were the only ones who managed to prove that hard work can beat bloodline and talent.' - Shirou.
As more months went by, it was finally time for the academy entrance test. Shirou received good news from Ishida. He found a place that might accept Shirou as a worker and help him learn weaponsmithing.
"To think I have to go to School again." - Shirou.