Typically, solenoid valves only operate as binary valves (either on or off with no in between). From what you are describing it seems like you want to proportionally control air flow using the solenoid valves, which will most likely result in rapid on/off switches to the solenoid valves.
It sounds like your PWM is at way too high of a frequency, where the voltage in the solenoid can not get high enough to actuate the valve. The goal would be to slow this down to a speed that allows the valve to open and close, but is fast enough to act like an "average" flowrate through the valve.
It might help to use the analogy of PWM control on a motor. In this case, the PWM motor voltage is analogous to the pressure (or the valve state), and the PWM motor coil current is analogous to the flowrate through the valve. Because fluidic systems are much slower than electrical systems, you won't be able to use conventional PWM frequencies.
As for the PID control, 3/2 valves can be dealt with as a single input to the system. An easy way to do this is to have a single input, single output transfer function, where a positive output controls flow from supply->common, and a negative output controls flow from common->exhaust.