I am at the beginning stages of planning an April 2013 trip to China . I first looked at the tours offered by China Spree and then read some of the comments on this site that indicate independent travel is doable in China. I much prefer independent travel over group tours. However, I would like to enlist the help of a travel agent in China who knows first hand the country and the best ways to get from place to place. Does anyone have a recommendation for a China based travel agent?

The company Wild China has interesting and different offerings, specializes in China, and has staff both in the US and many in China. They serve both inbound to China and outbound from China. They customize.

Not sure why you would need a TA for transit. Basically, either you fly or take the train. There are places you can only reach by bus, but it's very unlikely you'd be going there on a first trip. For info on train travel in China see http://seat61.com/China.htm

You should be able to do most of it yourself online. China is big and you will likely fly between cities. You can check domestic flights here ctrip.com and here travelzen.com.
Check the link above for train travel information.