You say the chime triggers when the wires are connected? It should chime when the wires become unconnected. When you twist the wires at the contact together that is like closing the window/door. As I am sure you know, the chime happens when the zone is violated (one of the doors of windows has been opened) and not when the window/door is closed. And it will not chime other window/door on that zone until all others are closed.
If there is only one 4 conductor cable at each contact and the cables in the panel are using all 4 wires we might be missing a splice point in between the contacts and the panel. I would have thought that the cable labelled Patio & Kitchen would have used red/black for the kitchen window because you indicate that the patio door was on green/yellow.
Can you start from the point of having the wires at each contact twisted together to see if you get a ready light? (just the ones that were replaced) This should simulate where you were before the windows/doors were replaced. In the beginning of all this you mentioned 2 windows and doors, I am guessing the patio door and the kitchen and dining windows, is there another door?
If you do get the ready light re-do one window or door at a time checking after each process.
If you do not get the ready light we must have missed something. Maybe try twisting the red/black pairs together at the affected door/windows to see if that gets you a ready/green light.
Have you operated the system since the work or tried to disarm the system twice in a row to reset it as mentioned earlier?
The fact that you are having an issue with zone 5 that was not touched almost leads me to think one of the cables got crushed or pinched during the window replacement process, hard to tell without getting into the panel and using an ohm meter to check for grounds and shorts to each other.