I can't help you with any ideas of my own, but I give credit to you and your group for looking for ways to take your fiancee' into the BW in spite of his wheelchair.  You're a special lady.

If he needs any assistance sitting in the canoe, there are adaptive seats being made by Kevin Carr at Chosen Valley Canoe Assessories.  Here's the website:  

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Give him a call to see if the seat might work in your fiancee's situation.

For any who may have wondered where we went, we ended up at Kawishiwi Lake. Just got back yesterday. It worked out well for us. I did call Wilderness Inquiry, they said most of their trips are on the number lakes out of Ely.  A few of us are going up to Lake in a couple weeks to check it out for a possible trip next year.
Thanks again to all for input and suggestions.

Hello TT, looks like I just missed giving advice but I'm glad you had a great time. I actually posed the same question over on the bwca.com forums earlier this summer. Some friends and I successfully took a disabled friend of ours on his first BWCA trip at the end of June. We ended up going Fall Lake to Basswood as others here have suggested. The portages are virtual gravel roads. The only downside is, of course, that it's motorized. How was Kawishiwi for accessibility?

Other routes recommended to us included the Numbered Lakes (an obvious lack of portages) and the Sawbill-Alton route over the old railroad line portage. I've personally not been to the numbered lakes so TT I'd be interested to hear about your thoughts on that, too. We're all already looking forward to our next trip.

Also, I want to second Jackfish. The trip was entirely made possible by Kevin Carr who generously let us use one of his adaptive paddling canoe seats. If anyone's interested, he has a site specifically set up for adaptive paddling seats he makes (by hand): (You need to Login or Register to view media files and links). Thanks Kevin!