Shirou's soul was revived and then transferred into Ilya's body when she used the Third Sorcery. "The container's a bit cheap (lacking), I can only use my own body, so I can't reproduce it fully". This would mean that when Shirou's soul is put into Ilya's body, Shirou's body wouldn't match his original body.
Here's about the soul: "Once you give it a container or a body, the soul manifested by the Third Sorcery will take perfect form". Because Ilya's Sorcery wasn't perfect, Shirou had Ilya's body size. Got it from here: "The Shirou Rider found was just a bit different from the Shirou we knew", "It's not like he'd grow if we watered him".
As for the magical energy left in the pendant, I think Shirou used it to draw strength into his body that was inside the Grail in order to get to the surface that was close. Ilya entered the Grail and her soul filled the Grail's power to perform a miracle, but her body remained inside.
Shirou reached out and lost conscioussness when some of his body was out of the water. In the epilogue it is mentioned that when Rider found Shirou "she picked him up... No, it was more like she plucked him out"
that would mean he was "plucked out of the Grail".
There were also speculations if Shirou's soul was transferred inside Rin's jewel, but this is wrong, because he wouldn't be holding it in his hand if he were inside it.
With backup from Kansho we concluded that Shirou was floating in the water of Ryudou Lake that flooded the cave. Most probably in one of the pieces of the Holy Grail.
The question that is still hard to answer would be:
"How did they move Shirou's soul into another body?" It was said that:
"Once you give it a container or a body, the soul manifested by the Third Sorcery will take perfect form. It's the genes of the soul, not those of the body."
"Souls can be put in the bodies to give them life, but the souls will be fixed to the body in exchange".
Shirou's soul overwrote Ilya's body so his soul should be bound to it.
Perhaps Ilya bound Shirou's soul to her body in a way so that Rin could move it somewhere else later. She did say: "You'll be back (to your old self) in no time if you and Rin keep trying".
It could also be that Shirou gained the ability to transfer his soul when the Third Sorcery was used. Rin did say "Well, he didn't need our help in the first place".
I have some more stuff to post, but I'll do it later.
Normal End IS depressing as hell. No arguments there. Especially when I first saw it.
I cheered myself up with the True End