[OxBlood]

As far as I know, it goes like this:

-Do all normal loyalty missions
Edit: -Get all upgrades for the SR2, sure, just forgot that, thanks for the reminder, Dimnos.
-Do Legions LM when you get it, do NOT do anything else before that
-Have a high enough Paragon/Renegade Score to settle the two disputes among the crewmembers

So basically, you have to do any sidemissions before you go get the specific part for you little spaceship, since that would lead to getting the last loyalty mission.