1:9-10 

... grace, granted to us in Christ Jesus before time began, but now made visible through the appearing of our Savior, Christ Jesus.

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Elsewhere, descriptions of The Father's plan—The Mysterion of God—are less specific. This one indicates Jesus by name. Humans did not exist in eternity past for The Father's grace to be granted to them, but The Logos through Whom the promise would be realized did exist. In Paul's day, He was made visible as The Son.

→ See The Mysterion of God

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1:18 

May The Lord grant [Onesiphorus] to find mercy from The Lord in that day!

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You read that verse correctly. The first "The Lord" is The Father. The second "The Lord" is The Son, the Eschatological Judge. This is reminiscent of Genesis 19:24, where the visible manifestation "Yahweh" calls down fire on Sodom and Gomorrah from "Yahweh in Heaven."

→ See Conflations, The Father and The Son

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2:7  

Apprehend what I am saying: For The Lord gives you understanding in all things.

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"The Lord" is likely the Holy Spirit, because there is a break with the next verse which reintroduces Jesus Christ, and since He is who performs this action in many other places [Neh 9:20; John 14:26; 1 Cor 2:13; Eph 3:5; 3:16; 2 Tim 1:8; 1 John 2:27]. This means that within 92 Greek words of each other, "The Lord" is ascribed to The Father [1:18a], The Son [1:18b], and The Spirit [2:7].

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2:13  

If we are unfaithful, He remains faithful, since He cannot deny Himself.

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Unlike humans, who think and act in ways contrary to their normal character, Paul says Jesus "cannot deny Himself," implying His immutability.

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2:19  

However the foundation of God yet stands, bearing this seal:

The Lord knows who are His

and

Everyone who calls on the Name of The Lord must stay away from evil.

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Paul cited Numbers 16:5 here, but changed the sacred name "YHWH" to "The Lord," and was referring to Jesus. This would be almost the highest blasphemy (the highest would be 1 Corinthians 8:6), if Paul was not including Jesus in the identity of Yahweh. It is clear that Paul equates Jesus with The Lord in this context; he wrote even more clearly about it in Romans 10:9–13, using the same element of "calling on the name of." 

→ See Lord

→ See Romans

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4:1  

... Christ Jesus, the One who will judge the living and the dead ...

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Everyone knows the Judge at The End is God. Here, Paul says it is Jesus.

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4:14  

... May The Lord repay him according to his works.

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Paul has been very careful to differentiate between "God" and "Lord" in 2 Timothy. In this verse, Paul makes a statement which conforms rather closely to Psalm 28:4. The one who judges humankind in 2 Timothy 4:1 and 4:8 was Jesus. In Psalm 28:4, it was Yahweh. Paul substitutes Jesus for Yahweh in an OT allusion or citation a second time.

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2 Timothy Summary

The Father provided salvation for humans by His grace even before He created them: His provision was The Son, who existed before time began [1:9–10]. Paul explicitly lists two Lords [1:18], despite being a monotheist. Jesus Christ, the immutable [1:18] Judge of the Living and the Dead [4:1], is cited in two Old Testament quotations [Num 16:5; Ps 28:4], substituted as Yahweh [2 Tim 2:19; 4:14].

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