1. Are you sure you had power to the track before you started cutting wires ?
2. I'm assuming you installed the switches in the track layout and tested them on track power to make sure they were all working properly with the controllers, before you started disconnecting and cutting the wires ?
3. I'm assuming you disconnected and cut wires because the wires were too short for the controllers to reach the switches or because you wanted to hide the wires below the layout (or both). Cardinal rule (at least in my book) is never disconnect the wires from the switch or especially the controller itself, if possible. Try to cut the wire in the middle and then patch the ends together using some sort of connectors (I like the gel-filled "bean" crimps) or you can buy 4 terminal phone connectors which you can mount to the layout and then connect up the wires.
4. Per #3, if you did disassemble the controllers and disconnect the wires, it is always a PITA to install new wires because of the tight space and configuration of how the wires go.
5. If the wires were installed incorrectly in the controllers then it's not going to make a difference whether they are track powered or powered from an alternate source - they still won't work.
6. I would start by making a small test track with a few pieces of FT and put each switch in one-by-one running off track power and check the controller wires to make sure they are hooked up to the correct terminal and making good contact.
