Tenacious,
Regarding Thomas worshipping Jesus (John 20:24-29). (Chapter 21 was added later.)
I do not know if you have studied the Christology of the Gospel of Thomas, but the people who wrote the Fourth Gospel ("John") had also developed their own Christology but had arrived at different conclusions. In this passage, the writers of John were reflecting upon the Thomasine community. Read the story again, this time realising that this is not a literal historical account but a story designed to denigrate the Christology of the Thomasines. This methodology is also employed at several other accounts in John, such as the mythical Nicodemus and the Blind Man who could now see.
Regarding 1 Timothy. It was written at the beginning of the second century (Paul died in 64 CE). At that time, a Gnostic named Marcion relied on Paul's writings, even producing the first collection of Paul's letters. Marcion made so much use of Paul's writings that the proto-orthodox gave Paul a wide berth.
The person who wrote 1 Timothy was complaining about the way that people (no doubt the Marcionites) were using Paul. In that context (early decades of the second century) attempts made against Marcion included the writing of Acts of the Apostles. (2 Peter is likely the last canonised writing, coming later in the second century, almost 100 years after Peter's death.)
Doug