get permit in Shanghai?

If you have related visa, you are allowed to stay in Shanghai and Xian for some days. But if you want to Lhasa, you still need the Tibet Travel Permit. You can not get one Permit, if you do not join a tour group.

We plan to come to Shanghai from NY on Sept. 29. We have China visa. We want to stay 2 days in Shanghai, 2 days in Xian, and go on to Lhasa and Kathmandu. Can we get the Tibet Travel Permit in Xian or in Lhasa? Do we have to be in a USA group to get on the train to Lhasa? Can you rent the whole room so that you do not have others in your train room? We want to stay a few days in Lhasa and go on to Kathmandu. Do we have to be with a group to go on to Kathamandu? Is it best to go over from Lhasa to Kathmandu or to fly? Thanks. Any information is appreciated.

Well, you need to get this permit in Xian, but you need to apply for it in advance. That means you need to contact with the travel agency in advance.
You do not need to join a group in USA, but a Chinese local tour group. You can find it in Shanghai or in Xian. Here I can recommend one for you. The TravelChinaGuide may help you to get a permit. You need to contact them in advance for help.
On the train, you can book a soft sleep with a door for each small room, so you will not be disturbed by the others. But you cannot rent a whole room for you.
If you want to go to the Kathamandu from Lhasa, you do not need to be with the group. Join a group is a way for you to get a permit. After your traveling in Lhasa, you can fly to Kathamandu from there.
I hope these information are very useful for you and help you.
Terry