The analyses of a text #1

The protagonist, Philip moved in with his uncle Mr. Carey, the Vicar of Blackstable after his mother's death.
He goes to the medical school St. Luke's in London.

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One morning Philip on getting up felt his head swim, and going back to bed suddenly discovered he was ill. All his limbs ached and he shivered with cold. When the landlady brought in his breakfast he called to her through the open door that he was not well, and asked for a cup of tea and a piece of toast. A few minutes later there was a knock at his door, and Griffiths came in. They had lived in the same house for over a year, but had never done more than nod to one another in the passage.
"I say, I hear you're seedy," said Griffiths. "I thought I'd come in and see what was the matter with you."
Philip, blushing he knew not why, made light of the whole thing. He would be all right in an hour or two.
"Well, you'd better let me take your temperature," said Griffiths.
"It's quite unnecessary," answered Philip irritably.
"Come on."
Philip put the thermometer in his mouth. Griffiths sat on the side of the bed and chatted brightly for a moment, then he took it out and looked at it.
"Now, look here, old man, you must stay in bed, and I'll bring old Deacon in to have a look at you."
"Nonsense," said Philip. "There's nothing the matter. I wish you wouldn't bother about me."
[Of Human Bondage by Somerset Maugham]
1. I'd like to know if "that" is implied before "he knew not why."
2. I'd like to know if "He said" is omitted before the clause in blue.
3. I'd like to know if "in" is implied before "the matter."
Thank you in advance for your help.