After nearly a week of messing about, I have finally managed to build the launch. While I'm happy with the results, there are some tiny gaps and at the bow end there is a small depression, so was wondering what the best way of filling them would be?

I would agree with Mr T, I am using two different fillers on my Victory, the Ronseal Multipurpose Wood Filler (natural colour) for simple filling of small gaps such as the half millimetre between the fenders and the hull, much the same as the small gaps on your launch. Once dry it sands down fine enough for most finishes, paint or varnish etc.
The other filler is Milliput two part epoxy putty which is like a sticky plasticene once mixed together, this I use for construction jobs rather than filling, it can be moulded or sculpted into shape, wetted tools or fingers can produce a very smooth surface which goes rock hard and can then be sanded, filed or sawn to shape.
If you look on my DelPrado build diary, on the photos of the completed stern, the bottom of the side galleries below the windows is all made of milliput.
For your launch however, I would definately go for the Ronseal, it was £2.99 for a 100gm tube at my local tool shop and it'll last a very long time!

Happy Filling!

Robin