When you say one zone- do you mean one wire run? So one wire per door, one per window bank? (I figure I can just use some phone or Cat5e/6 I have).
I would use real alarm wire, not cat5. If memory serves me it is 22 gauge 2 or 4 stranded.
And yes, I think you understand about the zone wiring. You should do a home run to each door and a home run to each bank of windows. Once you get to the bank of windows you daisy chain the windows together putting them in series electrically with your end of line resistor on the last one. Doing a home run to each individual wire is way overkill in my opinion and will result in a mass of wires that will just kill your day (or week, or month) trying to organize and hook up.
Also consider smoke detectors. pull 4 stranded for those. Also pull 4 stranded for you motions. Cat5 is good for your touchpads.