One thing that I learnt the hard way is that if you drill too far in advance, then the timbers can shrink a little before assembly which means that your holes will be too small. Redrilling them with a standard auger bit won't work as you just push the fibres apart. I split about 3 pegs trying to drive them home and one is still not quite out the other side.

Having said that, my timbers stood outside over the summer while I finished cutting the rest of the joinery so I don't suppose that my experience is typical!