When the upgraded character attacks, before you flip any cards and before your opponent triggers any 'when this defends' abilities, you look at the characters current attack value. If it is 3 or less, then you untap the character. Any additional attack you gain after that, be it via other 'when this attacks' options like Paralyzo Box, orange battle icons, or another effect, do not matter because they are added after the attack. Even though your character is untapped, it continues to get to do its attack.
Yes. In bot-mode, Wolfwire
's ability indicates that instead of the game concept of swapping a green battle icon, Wolfwire can put one in hand. While Wolfwire, with a Melee trait, is unable to swap a card for Paralyzo Box due to its Ranged hybrid green battle icon, it is still a green battle icon and qualifies for his ability.