You can set the page size in LaTeX with the geometry package:
You can also set margins and some other page-layout parameters with the geometry package.
By the way, 3.47" by 4.54" (88.2 mm by 115.4 mm) is the correct page size for a PDF formatted for the Sony Reader. I recall that the first version of Sony's manual for creating PDFs for the Reader gave the display size as 3.57" by 4.82". I found that when I made a PDF using those dimensions, it was nevertheless appreciably reduced when displayed on the reader. 3.57" by 4.82" may be the screen size, but it seems that to get the exact displayed "page" size, you need to subtract the area occupied by the status bar at the bottom of the display. The Sony manual later gave a corrected display size of 3.47" by 4.54" (88.2 mm by 115.4 mm), which I find works perfectly.