I was in Nepal last November by myself. It is a SWEET trip, how long are you going to be there and how big is your group? Here is what I learned:
#1 - Base yourself out of Pokhera, not Kathmandu. It is MUCH nicer and you can get everything you need as a westerner looking to kayak there. If you do end up in Kathmandu the local boater hang out seems to be a guest house called "Holy House" I believe and is about a block down and around the corner from the famous Kathmandu Guest house
#2 - Talk to a guy German guy named Andy that runs Shiva Outdoors http://www.treknepal.eu/
based out of Kathmandu. He can custom setup trips for you, hook you up with guides etc. He hooked me up with a guide named Kamal (sp?) and it was like $15 a day plus expenses and we ran the Bhota Kosi. He also setup a raft supported kayak trip of the Karnali that I think ended up being like $350. He also seems to have the best selection of available boats. While I did one trip as a tag along on a commercial raft trip I think private guides are the way to go especially if you have 3-5 people you can share the cost with and get it down to something like $5 a day.
#3 - I plan on going back, and when I do I plan on taking ALL my gear including a cheap "modern" play boat which they need. I think if you bargain well enough you could trade that play boat for rentals through the rest of your trip.
#4 - Learn to bargain. I don't think I did a very good job of that and while I paid very little for the trips I took from a US stand point, I'm sure I could have gotten better.
#5 - Buy a good medical evac/S&R type insurance. While I didn't end up needing it and I didn't buy it, I WILL next time because the state of the medical system is so bad as an american you can not even imagine. I was told to go to Malaysia if I got seriously hurt... Go to a travel nurse and get all your shots, Malaria is a concern in some areas as well.
#6 - Last but certainly not the least important, don't expect to be on a schedule, things WILL not go as planned. You must be willing to roll with the punches.
Just fyi, I got my airfare from denver to KTM for about $1400 in feb for a Nov. 1 departure and a Dec. 1 return. I paddled 21 days total I think on the Sun Kosi, Bhota Kosi, and Karnali. The entire trip cost less then $3000 for a month all in.
IM me if you want to talk more and I'll shoot you my phone number.