Both are okay if used as dialogue.

Both are correct. Both question are asking whether Tom wearing jeans yesterday. Please note that the second question, you need to use wore jean instead or wear because the question is past tense.

Both are fine.

The second one is right. Because “be doing something” means that you keep doing an action continuously. In this situation，the subject keeps moving. But Tom wears jeans，that is an ordinary state ， Tom won't keep doing this action of wearing jeans. That's strange. I hope you can understand what I'm talking (≧▽≦)