There are 2 quests in Rathpike I couldn't complete.1 is to find the father of the 2 goths(german warriors) sitting in the bar,and 2 is to find out what happened to the delivery for the fish food restaurant.In Valos I have to join the sisters and find out about the meeting near the lighthouse.
For the father you have to explore the BLack Steel village and ask around about strange sightings involving the mines. Theres a Bar owner that knows about it, when you get him to meet you in an abandoned building, just outside the Bar he will tell you what you need to find is in the building.
FOr the Sally's you have to go thru to the west of rathepike into the desert, go northwest you have to go thru the Rock desert until you get into Narfus village, again go around asking NPC's in and outside to gain some information.
YOu should see a Mercenary ina blue uniform outside the opening that will lead you into the ROck desert. This will give you the option of joining the Merc's group which seems to be important to finishing Sally's quest!
If you decided to join the Merc's in rathepike, you will not have to worry about conflicts between Pliny's and the Merc's
After you have done enough with the Merc's in Rathepike, you'll be asked to join up with the Offices in Narfu this gives you a chance to kill the large squid ruining the villages fishing economy, and prove to the Narfu Merc's that your not just a worthless women! Then go back to Sally's and mention why! (I dont think this registers as complete in the Quest Log then again it may in 15.2, but it is complete there's didn't seem to be any real conversation from Sally about it.
The light House is around (its not on the top on my head where exactly) you look around for it! But its there, it maybe the boat captain near the lighthouse he will give you a boat ride to the island where the sisters have their Church!