Very random thoughts but here's what I can remember:
Try and visit as many loft conversions as you can to get ideas.
It will be very dusty, especially with the break through and the plastering.
If you can afford it, go for optimal space, ie. dorma, to increase head room.
Put a skylight over the new loft stairs otherwise it will look gloomy and dark.
Don't scrimp on windows, go for as many as you aesthetically can!
Have a good idea of what plumbing fixtures you want. At an early stage, the plumbers will need to install some essential pipes, pumps, etc. so be prepared.
Have a landing and a door to your new level.
Put loads of power sockets in. tv and telephone points.
Try and match the style of staircase to the existing one. It looks very odd if it's different.
Be prepared for mains smoke alarm to be fitted on each floor. This may involve pulling up carpets in landing, etc.
Having said all that, it's well worth the disruption.