Hi, welcome to the site. Congrats on choosing a Focus, I'm sure you be happy with it.
For most of your questions, I'll let the professionals deal with them, but the one I can help you with is your PPS. I've never heard of such a penalty. If they try to include one, call them out on it.
2009 Vista Blue SE Coupe
FSWerks CAI, H&R Springs, FSWerks ECU, Sound Ordnance P-57 speakers, remote start