What is the paper size you're using?
When creating large PDF files you have to be careful
to specify the correct papersize (or make the PDF scaleable).
ps2pdf -sPAPERSIZE=a0
should create a nice A0 size PDF file that can be plotted.
I would rather avoid the step of creating an EPS file first
as it messes up the page bounding box.
What exactly is the problem of your PDF files?
Steffen