If you want to optimize your upgrades don't merge any purple dupe parts you get right away.

You'll be able to farm pic related from delivery missions, so you should do your upgrades like this using two copies of Arash as an example:
>Arash Base: Increase quality with Common Upgrade Kit
>Increase quality again with two Blue parts that are at Purple 2
>repeat above steps with second Arash
>Combine both Gold I Arash into a Gold II