1) about the wider body of the chinese CRH3: there is a video where the vice-head-engineer of the chinese railway ministry (???) Zhang Shuguang boasts on board the newly minted CRH3 on the Beijing-Tianjin line, in front of some Siemens engineers, that the chinese achieved "better parameters" despite the higher air density on the chinese line (than in Germany) and the wider car-body. The scene occurs around 1:41 in:

http://www.youtube.com/watch?v=mWwQsRWtveI

What this means is that clearly they were making modifications to optimize from the very beginning, otherwise one could reason simply the way you did, from the fatter train body (and the thicker air in china) to the implausibility of higher speed.

2) Your reference to the "Planned modifications and research" is a blog discussion in July 2009, about a book that was then already published (by the very Mr. Zhang Shuguang in the video mentioned above). So it is not clear if the modifications and research goals are still "planned", or are already (partially) realized.