Can someone explain me why my weapon with full orange upgrades give me less mastery and HP then weapon with yellow upgrades? Or it will change when i get 2lvl weapon?

Thats right, the upgrades for the Epic weapon depends on it's rank. For example a new rank 1 Epic weapon may give you only 7 mastery for clicks in red area, while a rank 4 may give you 10.7

So as you rank up one by one, every each of those upgrades on your epic weapon will become higher.

Have fun;)

So it's better to rank up the weapon first, and wait with the upgrading?

No, as I said:

No need to wait for rank 4 to start upgrading.

Hello,

Thanks for your answer, I think this will help lot of players , including my self !