I'm going to largely echo what others have said, I think. That is a very packed itinerary, but looks like it could fairly easily be cut into a western loop and an eastern loop. I'd do only one of the two loops. Either one has more than enough to consume many more than 40 days!
1. Two A/Cs shouldn't be needed. While driving, the dash A/C can also be used, and it doesn't sound like you'll be spending much time during the days in the RV when not driving.
2. Partly depends on your wife's comfort with driving in general, but a 31' unit on the highway is not too difficult to handle IMHO. To me, it seems like driving a U-Haul or similar, but with somewhat better visibility and much more comfortable seats. Maneuvering around parking lots and such is more of a challenge.
3. No. I'm assuming you aren't going to go off-roading with the motorhome.
4. I'm not a huge fan of slides (mostly a personal opinion), but they do offer much more space inside when camping. As others said, do make sure things are accessible in units with slides when the slides are in or they won't be accessible while en route or easily accessible when parked in many places. Slides do add to the weight of the unit, which may mean carrying less water and/or stuff.
5. Generator fuel usage is irrelevant when compared with the fuel consumption of driving (figure 8-9 mpg typically).
6. 11 hours of driving is a very lot in a day between campgrounds. Assuming only an hour for lunch and gas stops and such, that means leaving at 7:00 in the morning (and getting up well before that to eat breakfast and tear down camp) and arriving at 7:00 in the evening (and then setting up camp and eating supper.) Also bear in mind that a motorhome is not going to average as high speeds as a car; figure maybe 60 mph average on the interstates (or possibly a little less).
Assuming you do reasonable prep to the unit beforehand (as in tune-up sorts of things, getting new tires if they're old, etc.), you're unlikely to have much or any breakdowns that keep you from moving. More problems are likely to be related to the house part of the motorhome—the generator, water system, fan vents, fridge, and so forth. If you're handy, a lot of the problems tend to be things that can be fixed fairly easily without resorting to a repair shop, but certainly not all. (Little things like cabinet latches and blind cords and so forth....)
The Ford and Chevy chassis mostly used are also used on lots of other vehicles, mostly commercial vehicles, and are quite reliable overall.
7. Hershey park is great, but there are many other nice amusement parks/theme parks in Pennsylvania as well. Kennywood (in Pittsburg) and Knoebels (kind of in the middle of nowhere in north central PA) are two of my favorites—both rather traditional parks, and both with exceptional roller coasters among other rides.
I would suggest at least considering stopping at the Henry Ford museum/Greenfield Village outside of Detroit. The St. Louis City Museum would be a hit with the kids I think, too; it's hard to describe, but more a fantastic playground than a traditional museum. IMHO it's more fun for a day than Disney.
