Moving the HUD is easy...
/nui hud vofs {n}
where {n} is a number... this higher the number, the higher the HUD moves up. Try '/nui hud vofs 150' as a starting point then try different values until it lines up where you want.
As for the missile proc indicator... I'm not sure what that is you're talking about. Maybe a screen shot? (you can use the paperclip icon in the message editor to upload it directly to this forum)
You might also try using the comnand '/framestack' before the missile proc indicator appears then mouse over it as soon as it does so I can see the list of frame names that are there, and post that screen shot, too.