Hi Andrew,
I hope you know some very influencial people in high places with who you can pull strings or otherwise you may be very disapointed.
At the present time travel on the Nile is only allowed between Aswan and Luxor plus a little bit further down river to the temples around Abydos. This normally takes place on cruise boats which travel in convoy with armed escort. Felucas, the small sailing boats, also travel this route and for a fee you can have an enjoyable time on them, but, there is sometimes a hassle getting to Luxor from Aswan on then due to the Nile Barrage South of Luxor. The captain of these felucas can also be hassled by police on route for several reasons normally such as "Need mony for fuel as our boat has run out."
The authorities there are very touchy about lone travellers, they like to have everyone organised into official travell groups and convoys. You may be able to get permission to kayak from Aswan to Luxor as long as you pay the appropriate fees to the correct people, but, you have not much hope for continuing further down river.
Rob