I apologise if it's been answered before. but:
Upgrades: The required Normandy upgrades are new shields from Jacob, new armour from Tali and new weapons from Garrus. Either ask them about upgrades or unlock them for research by completing their loyalty mission.
The Mission Itself: Everyone needs to be loyal if you want to guarantee everyone alive. If you made it to the base with no casualties then you have all the necessary upgrades.
Your specialist in the vent should be either Tali, Legion or Kasumi, assuming that they're loyal.
Your fire team leader should be either Garrus or Miranda, assuming that they're loyal.
You must hit all the vents before your specialist is killed. If you made the right choices, then everyone should be alive when you proceed to the processing chamber. If you went through the Omega 4 relay immediately after your crew were kidnapped, you should save them all.
Your biotic specialist should be either Samara or Jack, do NOT pick Miranda per her suggestion, only Samara and Jack will save your team, assuming they're loyal.
Your fire team leader should probably just stay over from your first choice, for example Garrus.
To escort the surviving crew to the Normandy, pick Mordin. Even if he is loyal, he has a chance to die randomly during the final battle. Each character has a defense rating, Mordin's is one of the lowest.
Everyone should still be fine when you reach the final battle. Take whoever you want, but they must be loyal. If not, they will die after the final boss.
Using this guide, everybody should survive.