Here are the answers to your Scriptures:
Prov. 16:4 The Lord made the wicked man but did not cause him to be wicked. The Lord made the man good, and the man made a different choice. That is the reason the next verse explains how the man got that way. And that is also why He made the man for the day of evil. It's on that day that the wickedness will be exposed.
Is. 45:7 Remember this is poetry also. Read in Hebrew, you get the proper sense. I form (yatsar=to mold) light and create (bara=to give meaning to) darkness. So the first part of the poetic couplet sets us up that by molding light into a useful form, God causes us to recognize darkness. Compare this to Gen. 1, where when God "bara" earth, He first made light, but darkness already existed. The second part of the couplet is I make (asah=make happen) peace, and create (bara) evil. The parallelism is obvious. Evil is known because of peace, just like darkness receives meaning because of light.
Amos 3:6 The evil referred to here is the punishment for sin, which men call evil. This is clear from the context. Job 2:10 is related, evil comes from the hand of the Lord; He does not create it, but He does apportion it properly to correct His children. That is why the next verse also speaks of the prophets knowing what will happen ahead of time.
Lam. 3:37-47 is the detailed explanation of all these passages.
Eph. 1:1 is not applicable, since evil is not a thing, but the absence of a thing.
Rev. 13:13 is not applicable, since fire is not inherently evil. Ps. 104:4 says angels are made of fire.
God does not create evil. Our sin creates what WE call evil. He does use what we call evil to wake us up to our sins.
There is no use trying to disassociate God from evil, as you are trying to do, because God is the very creator of evil in the first place.
"I form the light, and create darkness: I make peace, and create evil. I the Lord do all these things" (Isaiah 45:7)
Yes, even evil (which in Hebrew means: misery, affliction, hurt, harm, calamity, adversity) is the creation of God. He has not only created it, He can even use evil in the pursuance of good. However, it must be clearly understood that only a sovereign God can do this. That's because His omnipotence allows Him the full capability of bringing good out of any evil. We humans have no such power. God orders us to shun evil at all costs (1 Thessalonians 5:22). But God certainly uses evil in the accomplishment of His plan. One of the greatest evils ever perpetrated by the hand of man was the crucifixion of God's own son on the cross. Yet that very evil was planned to occur before the foundation of the world (Revelation 13:8). All the actions of God (both good and evil) have a purpose, which God is using for the final good and glory of His creation. He has a "plan of the ages" (Ehpesians 3:11, Greek). The center of that plan rests in the actions of Jesus Christ and in the redemption, which is found in the efficacy of His cross and resurrection.
"See now that I, even I, am he, and there is no god with me: I kill, and I make alive; I wound, and I heal: neither is there any that can deliver out of my hand" (Deut. 32:39).
Let’s delve further. Twice Joseph acknowledges that his brothers sold him into slavery in Egypt. Yet he declares that their thoughts and actions were not really their own but God's work. "So now it was not you that sent me here, but God." How had God done that? He Himself tempts no man so He had sent an evil spirit to cause that thought to be conceived and carried out. Just as He withdrew His own spirit and then sent His evil spirits to trouble King Saul and to cause King Saul to want David dead, and just as He sent a lying spirit into the mouths of all of King Ahab's prophets.
1Sa 16:14 But the Spirit of the LORD departed from Saul, and
an evil spirit from the LORD troubled him.
1Sa 16:15 And Saul's servants said unto him, Behold now,
an evil spirit from God troubleth thee.
2Ch 18:21 And he said, I will go out, and be a lying spirit in the mouth of all his prophets.
And the LORD said, Thou shalt entice [him], and thou shalt also prevail: go out, and do even so.
2Ch 18:22 Now therefore, behold,
the LORD hath put a lying spirit in the mouth of these thy prophets,and the LORD hath spoken evil against thee.
Here is God's answer to all who confront Him on this question:
Rom 9:17 For the scripture saith unto Pharaoh, Even for this same purpose have I raised thee up, that I might shew my power in thee, and that my name might be declared throughout all the earth.
Rom 9:18
Therefore hath he mercy on whom he will [have mercy], and whom he will he hardeneth.
Rom 9:19 Thou wilt say then unto me,
Why doth he yet find fault? For who hath resisted his will?
Rom 9:20
Nay but, O man, who art thou that repliest against God? Shall the thing formed say to him that formed [it], Why hast thou made me thus?
Rom 9:21
Hath not the potter power over the clay, of the same lump to make one vessel unto honour, and another unto dishonour?
The answer is that no one can resist God's will, and He is working all things according to the counsel of His own will, and if we don't like the way He is doing things, then that too, is His work. All of our thoughts, good and evil, are His work via either good or evil spirits, and in the end it will all "work together for good".