I can to renumber the runways or add new ones in PFE?
No, you cannot do that in PFE, and like I said above you would not want to, otherwise you be told to take off from a runway that does not exist.
You can however edit the airports in FS9 to change the runway numbering/add new runways/change navaid requencies or add new navaids. Then when you run "makerunways" PFE will have the new information in its database.
You need to use ADE (Airport Design Editor) to edit afcads in FS9 and make sure you backup your files first. You will need to do some research as I think if you add a new runway you may need to add "approaches" also or PFE may have trouble directing you to the new runway. You will also need to add taxiways, so this is no small endevour. I would experiment with a small default airport first that has only one runway, which you can "close" after you add another to test your work.
To be honest I am not sure it is worth it....your new runway is going to look very odd if it ends up in the middle of a field !