To be honest with you, the longest trip my wife and I had together was 150 miles on a Ducati Monster. Naked bike + tiny seat = not fun.However, the longest I have ridden solo was Washington DC to Key West, 3000mi round-trip on the Monster with no windshield.
Part of the reason I bought the FJR was to remedy the discomforts of a naked bike and to enable us to take comfortable trips together.
I should say that my wife is pretty enduring when it comes to physical comfort. Her petite frame (XS jacket size) allows her to get very cozy in car seats, planes and generally finds any seating/sleeping arrangements comfortable. She assures me she'll be fine on our long trip. I on the on the other hand have less faith in my own physical comfort as I have a bad back, bad shoulder and get pretty moody when either start to ache.
Regarding butt-monkey, I was thinking of borrowing a pair of Airhawks from a friend.
Personally, I would recommend that you and wifey take a long 2 or 3 day weekend or more trip with mileage each day slightly higher than you're going to attempt on your two-week trip. Call it a shake down cruise...put yourself in the same all day riding fatigue settings you will be in on your long trip. After you get back, talk to wifey about what worked and what didn't. Ask yourself AND her truthfully...was the daily mileage comfortable? Could I have done this for 10 or 11 more days straight.
I just say this because...I can do 700 miles and be good...but tired. The few times I have had wifey on the back, I am done at about 300 to 350 miles.
Best to find your limits before the trip.
If you and your wife still felt good after this shakedown trip, I would still have a backup plan just in case you decide you need to do less miles, one of you feels sick, etc. There's lots to see in this country...and you don't have to kill yourself to get some place first time out of the box. Quite frankly, it takes me a few trips to get my body saddle ready for a long trip.
Auburn, Wheaton
I tried riding with bicycle shorts a few times (padded around crotch/butt area) to place more cushion between my butt and the seat, and to be honest it felt horrible.
I personally would feel uncomfortable in padded shorts...wouldn't like the feel. However moisture-wicking shorts are a must.