There aren't really any indicators as such for a worn cone, only that the diameter gets very small and you have to use a lot of pressure on the pedal to get drive. Does it look like the sheaves have been moved on the shaft? that usually indicates that the cone is worn and someone has adjusted to suit.
There are bearings on the cone shaft, the upper drive disk shaft, and the rear axle that can be seized or worn. the chain if dry or worn can make similar noises.
What I would do is jack the rear end up so the wheels are off the ground, turn it by hand to try and find the culprit. then maybe drop the chain off, that will isolate the shafts a bit better.
They are easy to do in some ways, no gluing like in a greenfield for example, not a 5 min job either though, the whole yoke i guess with the cone on it needs to be dropped out so you can get the shaft undone to replace it.
