If I were to try and send PWM over twisted pair, I would take each PWM signal, feed it to a differential driver, and then connect that to a twisted-pair. So, you could get four at most in a single Cat5 cable if you do it this way. This is assuming a PWM frequency of <100kHz or so.

What I get from your question is that you have a bunch of remote boxes that contain LEDs that are driven by some type of transistor array that respond to the input PWM signal. My initial thought is to "up-layer" your problem / design such that instead of sending PWMs over a long distance, you send a command via some bus (RS-422/485, CAN, etc.) to each box saying "go to PWM x", and then inside the box, the path for the PWM to its driver is very short. This way, you can send your "real" information (desired PWM duty cycle) in a potentially error-correctable, resilient form over long distances. A local MCU or processor than takes it, and generates the requisite PWM signal with a short trip to the LED drivers. I realize this increases complexity, cost and requires more hardware.

As for distance limits, if you do what I suggested and utilize a RS-422/485 based system, you can reference application notes on that subject that can describe the network in terms of termination, maximum unit-loads, and distances -- TI has a [RS-422 design guide][1] that is useful. If you have many boxes that do the same thing, RS-422/485 will let you do "multi-drop" as well, and you can have many nodes tap-off the signal as needed.

**EDIT**: I see you updated your question:

1. I would not send two separate single-ended signals down a twisted-pair. So in a conventional Cat5 cable, I would say you're limited to 4 unique signals. Use the shield as your ground return, or sacrifice a pair for ground.

2. The number of signals shouldn't matter as much if you follow what I said in #1.

3. Yes, there is a practical distance limit. It will depend on how you choose to send the signals (i.e. if you use RS-422/485, reference that specification / app notes)

4. You should use each twisted pair in a differential fashion.

5. I wouldn't separate the transistor arrays from the LEDs by a large distance, because then you're going to have high currents switching over a long distance which is not a good idea.

  [1]: http://www.ti.com/lit/an/slla070d/slla070d.pdf