Hi!
I did a similar circuit around Lake Erie myself about two years ago. Crossing at Fort Erie shouldn't be a problem. There is a nice state park on South Bass Island where you can camp provided you don't mind taking a couple extra ferries to do the extra island.
It was a fun ride and I expect that you will enjoy yourself immensely, I know that I did! I went around Lake Huron last summer and this summer I am planning on going around Lake Ontario.
You can find links to both my Round Lake Erie and Round Lake Huron journals on the following page:
http://www.bicycletouring101.com/AboutTheEditor.htm
BTW: I didn't ride it but I seem to recall seeing a rail trail on an Ontario map that starts just South of Windsor and ends somewhere near Leamington. It might be worth a look.
~Jamie N