Now that the first step is complete, I can finally move forward with the plans I created during the 2 year wait. I call it my "Shirou Development Plan". It mainly focuses on the 4 aspects of magecraft, martial arts, knowledge and mental state.
Kiritsugu doesn't want Shirou to become a magus, and so will deliberately teach magecraft in a vague way, the wrong way, or just not teach at all. He will also not be spending a lot of time in Fuyuki because of his Illya retrieval missions to Germany. This means that Shirou will basically have to figure out most things on his own. Fortunately, unlike other systems of magecraft, Shirou's specialty of Material Transmutation doesn't really have complex rules and the way to improve it is well described in the lore.
Material Transmutation can be divided into the 4 parts of Structural Grasp, Reinforcement, Alteration, and Projection. Structural Grasp is the foundation of all the other abilities as you need to understand the material world in order to strengthen, change or replicate it. In the three years before Kiritsugu's death, I plan to have Shirou mainly focus on Structural Grasp and improve it in 4 directions:
1) I want to improve the way it is cast. Normally, Shirou would need to touch the object he wants to use it on to cast the spell. But later, we see he can use Unlimited Blade Works to cast the spell with just his eyes by looking at the object. Of course, this only includes swords and other weapons, but Archer has shown himself able to project things like high-tech fishing rods with a computer attached and cotton candy machines; and even Shirou was able to project electrical appliances in his shed years before the grail war that remained until then. Since Structural Grasp is the preliminary step of Projection, it should definitely be possible to improve it in this direction with practice.
2) I want to expand the range of targets to Shirou himself. Being able to use Structural Grasp on himself will help with body awareness and martial arts training. It will also be extremely useful for reinforcing himself and specific parts of his body later. But the most important thing is that it will lead him to discovering Avalon. It may be useless now that the last of Saber's magical energy was used to save him from the fire, but it is still a noble phantasm and an excellent practice tool for Projection. Its history will also familiarize him with Saber and lead him to ask questions about the grail war from Kiritsugu (though I hope to have that happen closer to his death).
3) I want to increase its precision and magnification. Reinforcement works by filling in "openings" in the target objects with magical energy. In order to find these openings, one needs a deep understanding of its inner structure. If the openings are overfilled or not properly located, the object will take the magical energy as poison and explode. Although he probably won't be able to reach the molecular or atomic level, increasing the precision and magnification of Structural Grasp even a little more will allow him to find more openings and increase the success rate and effectiveness of his reinforcement.
4) I want to extract more information from the objects. This one is the most important because it concerns his Projection. The reason that Shirou's projections are so much better than normal projections is because normal Projection only imitates the material composition and design of objects through the caster's imagination, while Shirou's Trace Projection also copies the concept of creation, method of creation and the accumulated history of existing objects. This allows Shirou to replicate the magical abilities of mystic codes and even create extremely stable ordinary objects that won't fade with time as shown by the electronic appliances. Shirou can easily extract this information from swords and other related objects thanks to his origin and element, but it should be possible to expand this ability to other objects with training.
In addition to Structural Grasp, I also plan to have Shirou practice Reinforcement during those 3 years to try and get him to reach the same level as or surpass the original Shirou before the grail war. This mainly involves the success rate and effectiveness of using Reinforcement on external objects and weapons. After Kiritsugu's death, Shirou can begin practicing something far more dangerous and risky, which is casting Reinforcement on his own body. Apart from the obvious like increasing his strength, speed, and durability, it can also strengthen his senses and (possibly) his natural healing.
The original Shirou didn't rely on reinforcing himself during the grail war to fight at a superhuman level. He actually relied on his Projection to copy the stats of the original wielders of the noble phantasms he recreated. When he projects a weapon, he can not only access the skills and techniques of the previous wielder of the weapon through its history, he can even recreate the strength and speed needed to perform those skills and techniques. This was how he cut through Berserker in the Fate route, fought evenly with a reinforced Kuzuki in the Unlimited Blade Works route, and performed Nine Lives Blade Works in the Heaven's Feel route. But there won't be any heroic spirits to copy from until the grail war and this method is unreliable compared to just reinforcing himself. He may not be able to reach Caster and Kuzuki's level, but he should at least be able to match Rin.
If Shiro practices his Projection while Kiritsugu is still around, Kiritsugu might dissuade him from continuing by calling it "useless", especially if he notices what is different about Shirou's projections. That is why it is better to wait for the 5 years after his death to begin training. Starting from learning the 7 steps of Trace Projection, to getting him to visualize the hill of infinite blades early, there is a lot of work that needs to be done. I also want him to learn of the copying skills aspect through learning the kendo skills of Taiga and others to learning knife skills from chefs. By the time of the grail war, I hope he can project stable copies of all the furniture, clothes, appliances and other objects in his house that won't fade.
Alteration is the one that shall be saved for last when it comes to training. The official lore is vague on this spell, but there seems to be 2 different types of alteration. The first type is just an advanced form of Reinforcement that uses the magical energy poured into an object to change its physical shape. This is how Archer turns swords into arrows and Shirou turns a tree branch into a bow. The second type seems to be an intermediary step between Reinforcement and Projection that allows the user to give an object a property or effect it didn't have before. A character in the El-Melloi 2 novels uses it to give arrows the ability to freeze things, emit lightning, and corrode metal. The first type should be easy for Shirou to learn, but the second type has never been shown being used by Archer or Shirou. That said, it is supposed to be the step in-between Reinforcement and Projection, so if Shirou masters those two first then he should be able to figure it out with trial and error.
For martial arts training, the first step is to have Shirou keep training Kendo after Kiritsugu's death. I don't expect him to reach anywhere near the level of a heroic spirit before the grail war, but he can at least try and reach the level of Taiga, who is said to be as skilled as Shiki Ryougi from Kara No Kyoukai. This would be difficult for normal people as Taiga is said to be a prodigy, but Shirou can simply trace her shinai and learn her kendo style directly. Of course, their builds are different so he won't be able to replicate it perfectly, but he can make up for it by following around Taiga to meet other skilled kendo practitioners and tracing their shinais as well. After Kuzuki comes to Fuyuki 2 years before the war, I can try and make Shirou trace his clothes or something to learn his "breathing and walking" skill. It definitely won't be perfect, but even a fraction of success may help Shirou's martial arts and magecraft improve.
It may also be possible to go to museums and find old swords used by skilled swordsmen to copy, but this is highly unlikely. Even in the real world, many of the things on display in museums are fake or imitations. In the Nasuverse, where mystery grows stronger the older it gets, most if not all the real ancient artifacts should be in hands of magic organizations and powerful families. Hoping to randomly stumble upon the swords of Miyamoto or even Okita are a pipe dream.
In regards to increasing Shirou's knowledge, I am planning on having him focus on learning about chemistry and biology. His magecraft is material transmutation, so it is reasonable to believe that having more knowledge about the material world will be beneficial. On that note, it's probably important to have him study physics and math as well. Learning English is also important for going abroad but that is lower on the priority list.
Finally, there is the hardest task of trying to improve his mental state. Shirou is suicidal, traumatized, and believes he doesn't deserve to be happy. His obsession with becoming a "Hero of Justice" is a way for him to ignore his past and helping others is a way for him to "atone" for surviving. I am not a therapist, but I do know how he grows as a person during all three routes. In the Fate route, he learns to accept the past and embrace the future. In the Unlimited Blade Works route, he accepts that his ideals are unattainable, but chases after it anyway because it is beautiful. In the Heaven's Feel route, he chooses to prioritize his humanity and emotions over his ideals. I can use his dreams to try and direct him in these directions and teach him these lessons. However, Shirou is an extremely stubborn person, so I probably won't be able to change his mind too much in regards to these things. The best I can do is try and lay a foundation so he accepts these things faster during the grail war.