Yes..... go!!!!!! It's going to be awesome. I do a daddy/daughter trip each year with one of my daughters. We alternate each year which one goes with me while the other one stays home and does cool stuff with mom. They each did their first trip with me when they were 5 and now they are 14 and 12. They both look forward to their next trip starting on the drive home ;)
My younger daughter is also high functioning autistic and she has been amazing on each of her trips that she has done with me.
I always basecamp on my trips with the kids. Each year I do give them the option to do a travel route, but they both continue to want to basecamp. Exploring and playing around camp and fishing are their 2 favorite things to do so a basecamp gives them the most time to do those things.
Include them in the planning and let them help with decisions. It is their trip :)
My girls always carry a light backpack and even when it was all of us and they were in the 3rd seat of the canoe they each had their own small paddle. They need to feel like they are pulling their weight on the trip ;)
I don't know campsite info for Duncan/Rose but I have daytripped by canoe to the Stairway Portage/Rose Falls by canoe with the whole family and my wife and I have hiked to it on the Caribou Rock Trail. Rose Falls at the Stairway Portage is definitely a must see while you are there. Also... the Border Route Trail cuts right through the portage from Duncan to Rose so you can leave your canoe there and hike part of the BRT and it has some awesome overlooks of Rose Lake.