The header page contains div#siteCenter whose width is set to 926px which is 9.56'
The width of the PDF printable area is 8.3' - 2*0.75 = 6.8' so the header page is scaled down to ~71% to fit the PDF page. That's why the header comes out smaller.
To fix this, you need to make the header page width smaller or equal than the PDF printable area width. Even better would be to use an HTML fragment containing only the header code instead of the whole web page.
Regarding the timeout error, we will take a closer look at it and update you once we know the cause.