Couple of things:

1. It says all armour is required; does it need to be fully upgraded? Cause some of those upgrades requires scales from the dragons, which aren’t allowed to be collected.

2. It makes no mention of All’s Well, is that also required?

it is all armour but none needing to be upgraded, and the All's Well is attached to a quest so it's also required for 100%

Awesome, thank you so much :)

How about the recipe book?

The recipe book is not required for 100%

You're allowed to collect things from the dragons, as long as you don't use Intro Skip.