The only time you might rub - with stock or aftermarket suspension - will be when you go over bumps, through dips, have a lot of weight in the car, etc.
I still have a little rubbing with the fender well lining, but not much.
Can't say whether or not you should go with 40s or 35s - depends on the style of wheel really. I think my wheels would look a little funky with 35s.