completely rewiring a house after it's built is pretty difficult if you care about how it looks. The best case would be to reuse as much of the existing wiring as possible and just replace components like magnetic contacts, motion detectors, keypads, and the control panel. From the sound of things you've made this more difficult that it needed to be and you may have damaged things and you likely no longer have any idea what's on a particular zone.
Post some pictures of the state of your alarm system including the components you removed and components that remain. It would also be helpful to list the zones and what's on them, known issues with particular zones, and a bit more about the house (size, number of stories, basement/crawlspace/attic). Info about your skill level with electronics and construction would also be useful.
If an alarm is installed at construction they typically use recessed press fit sensors that you don't see unless you open the window or door.
