DisneyCrazyMom,
My last visit was December 2000 when I stayed at Wilderness Lodge with my Electric Wheelchair.
I know that LisaPooh has reported a problem getting on and off the big ferry that goes between TTC and MK with her own chair (a Jazzy, I think), but I didn't have a problem with my Invacare that I couldn't solve with a good run at the ramp. Parts of the ramp are too steep to get restarted on if you stall. Keep the power on and you should be OK!!
The Wilderness Lodge is a different route altogether, using different docks. There are two types of boats, the smaller one requires you to step down to the deck, and the larger one, though having level entry at Wilderness Lodge and Contemporary may not have level access at Magic Kingdom dock. Unless things have changed since last December, the only way from Wilderness Lodge to MK, is to ask the captain of the larger boat to divert to Contemporary, and take the Monorail from there. If the small boat comes is on the route, ask him to radio the bigger boat and have him divert to WL to pick you up.
This is a *BIG* pain. You would *REALLY* have to want to eat at Wilderness Lodge. Wheelsie's advice is good. Getting from WL to MK in a wheelchair is about the slowest resort to park trip anywhere at WDW if you have a wheelchair.