I didnt even know about Achievemnts till I was about level 20, but I used them for everything casue I enjoyed the team dynamic. As far as I know I followed the main quest and only started sidequest after getting Liara, and even if I did a few around the area of Liara's digsite I know I had Wrex with me before diversions.
I am not keen to play through the whole game with them again. I am thinking downloading "Bring Down the Sky" might solve my problem?
Also, while I doubt this, I know that other achievements requirements use the data from all profiles, eg. I can use Overload with one profile 50 times and then use it 25 times with another profile and I will have the 75 uses needed to unlock the achievement. I dont suppose the same is true for Allies? If I continue my profile in a new game starting with level 50 can I do the sidequest with them there to get the achievement?
Thanks!