1. Is there a use for the hourglass in Chapter 1? Perhaps I did get a quest but I've forgotten it along the way?
Yes, it's a side quest that starts in chapter 1 and finishes in chapter 2
Wessar Empty house -> Hourglass
Alcim -> Back to Hramm Cold Hand -> Swap to get the Clock
In Kian (Chapter 2) you get the Cristal Ball
2. Is there a use for the Rune of Ing in Chapter 1? Perhaps swap it somewhere for the Rune of Eolh and give it to the rune collector?
You did good the remaining side quest is in chapter 2
3. I have a question mark next to the fountain in Alcim - is there an outstanding quest or is this one for Chapter 2?
Nop it's mainly to spot the fountain
4. There is also a question mark next to Theo's house - but this may be because there are more things for him to mend in Chapter 2?
Indeed
5. I still have a fish in my inventory even though I know I've finished this quest - though this may be a minor glitch!
Indeed I fixed it