Do I need to complete the full side story quest to revisit them, i.e i need to change my items, Rappy Wing, S-Beats Arms etc with the doc? If this makes sense?
Yes, if you turn in a side story quest at the quest counter after completing it, you'll have to complete all the other quests to be able to revisit the completed one again.
You can use both "Dr. Osto's Research" and "Unsealed Door" to convert your enemy parts, though (I believe), so if you've finished the first the second should now be available. If you've finished both, you'll have to do all the other quests again.
Or you can just unlock the process on a different character (or difficulty level on the same character), which will probably cost you less time anyway.