I just saved the Salarian Ark and I feel like I'm back on a linear track like you said. I'm definitely doing the Ryder's Family Secrets. My biggest issue is the "menu" and everything else is so hard to figure out. I haven't even bothered crafting or buying/selling stuff. It's so non-user friendly. I came to the conclusion last night that I don't have to buy, sell, craft, etc. because so long as I upgrade my weapons via pick ups I'm kicking ass through the story just fine. It's just all a bit confusing to me.