Cannot continue main storyline quest (Spoilers in description!)

[Enkidoh]

If I remember rightly, Cid should still be standing out in the Fogfens south of the entrance to Castum Centri (down in the swampy area), who will send you back into the Castrum instance if you speak to him (remember to keep your Imperial disguise equipped, as Cid's icon will not appear if you don't have it equipped).

I remember this when I did that quest as I wiped on the boss fight where you have to free Minfilia and had to home point. Thinking I was stuck I was surprised to see Cid there with the 'important NPC for your quest' icon above his head, and after speaking to him I appeared automatically back inside the instance (I had to do the boss fight against the Garlean troops from the beginning though). I can't remember the co-ordinates he should be at though so you might need to do a bit of searching in that area to find him.

Good luck!