I have gotten a lot better at manually scooping in it since my original post; no limpets installed for the last 2 ranks on my quest to unlock Lori Jameson (which I finished 2 days ago \o/ ). This advice is solid, and what I had ended up figuring out on my own...still have to point just a tiny bit "above" the item I'm trying to pick up though or the nose of the ship hits it. Once close enough that it is under the ship, then I can align normally. It was that bit about the ship hitting it that was giving me fits initially.
Turns out to have been great practicing in the FDL for more than just the FDL as well. I got a Cutter yesterday and scooping in it is similiarly impacted by the nose of the ship. My previous FDL scooping prepared me well though and I hit up like 20 or 30 HGE's while flying the Cutter around to get it engineered. I probably should have just put a collector limpet controller in it when I started the route...but I didn't.
I do still like using limpets though if I'm going to do a lot of gathering in space...not because I can't scoop, but because I'm lazy.