ACV circuit tracers come in all sorts of price ranges, and often, the less expensive ones can find an issue fairly easily, and the more expensive ones aren't needed. Some of the features of the more expensive ones are the ability to detect how far away a break in the cable is, but if there's no break, tracing which end is which and where it goes is fairly straight-forward. I've seen them for in the $20-30 range on the low end.
While things often get used in a different manner than designed, a cable with a red wire in it is normally best used where the red indicates a switched lead (i.e., goes through a switch to power something - IOW, not always on). If you don't see a red wire in the breaker box, it's probably being used for that functionality - a switched hot lead - fairly common for an overhead light fixture, but could be used for a switched receptacle and other things, as well.
You need to measure the voltage at the power panel for the circuits. If you remove the lead connected to the circuit breakers in question, then turn them on, what voltage do you read?
Also note whether there's a 3-wire cable...is that where you see the red wire? If there was a double gang breaker there, and you replaced it with two single ones, you may have created a dangerous situation. It could have been a shared neutral circuit. If so, if there's a problem on one leg, the handle will make the other leg trip as well. I, for one, am not clear on exactly what you have, so trying to help is tougher.