Thanks for your trip report!
My trip to Venice with a manual chair a couple of years ago was also surprisingly do-able. We took the vaporetti, and found the crews very capable of popping the manual chair on and off quickly and safely. It was also cheap, free for me as a wheelchair user and 1 Euro for my husband as my companion.
The commune of Venice provides a set of maps showing wheelchair accessible routes in Venice that you can pick up at the tourist information office at the train station.