I see you can buy a leather dash top from Mini Genuine parts. How difficult is it to remove the top of the dash (under the wind screen) in a car with Nav?

Depends.

R50/R52/R53 you pop the plastic trims off the ends of the dash and it was something like 4 scrrews and it was off.

I had a go at my R56 the other week spent 3 or 4 hours pulling stuff apart and gave up :(

There may be some useful info on Mk2 dash dismantling in the pdf linked below:
'Chrome Line' Interior Trim - DIY Retro-fitting - Forums (http://forum.minicooper.org/showthread.php?t=13459)